I did some digging, to find out just who these "hate groups" Chick-Fil-A contributes money to are, to try and see what the fuss is all about. Turns out, the major offender is the Family Research Council (frc.org).

The Southern Poverty Law Center (splcenter.org) says the FRC is evil and immoral. From the SPLC website:

http://www.splcenter.org/get-informed/intelligence-files/groups/family-research-council

The Family Research Council (FRC) bills itself as “the leading voice for the family in our nation’s halls of power,” but its real specialty is defaming gays and lesbians. The FRC often makes false claims about the LGBT community based on discredited research and junk science. The intention is to denigrate LGBT people in its battles against same-sex marriage, hate crimes laws, anti-bullying programs and the repeal of the military’s “Don’t Ask, Don’t Tell” policy.
Hmm. Here's the FRC's mission statement, from their website:

http://www.frc.org/mission-statement
Family Research Council (FRC) champions marriage and family as the foundation of civilization, the seedbed of virtue, and the wellspring of society. FRC shapes public debate and formulates public policy that values human life and upholds the institutions of marriage and the family. Believing that God is the author of life, liberty, and the family, FRC promotes the Judeo-Christian worldview as the basis for a just, free, and stable society.
Their Issue Statement on homosexuality:

http://www.frc.org/human-sexuality#homosexuality
Family Research Council believes that homosexual conduct is harmful to the persons who engage in it and to society at large, and can never be affirmed. It is by definition unnatural, and as such is associated with negative physical and psychological health effects. While the origins of same-sex attractions may be complex, there is no convincing evidence that a homosexual identity is ever something genetic or inborn. We oppose the vigorous efforts of homosexual activists to demand that homosexuality be accepted as equivalent to heterosexuality in law, in the media, and in schools. Attempts to join two men or two women in "marriage" constitute a radical redefinition and falsification of the institution, and FRC supports state and federal constitutional amendments to prevent such redefinition by courts or legislatures. Sympathy must be extended to those who struggle with unwanted same-sex attractions, and every effort should be made to assist such persons to overcome those attractions, as many already have.
An opposition to the gay agenda in politics is not an attempt to "denigrate LBGT people". At this point in their presentation, the SPLC seems to have no basis for their accusations. Let's continue.

http://www.splcenter.org/get-informed/intelligence-files/groups/family-research-council
To make the case that the LGBT community is a threat to American society, the FRC employs a number of “policy experts” whose “research” has allowed the FRC to be extremely active politically in shaping public debate. Its research fellows and leaders often testify before Congress and appear in the mainstream media. It also works at the grassroots level, conducting outreach to pastors in an effort to “transform the culture.”
Yes, the FRC, on the Issue Statements pages of their website, and in their political activities, employ quite a few researchers, links to their work are provided on the Issue Statements pages, as linked to above.

 First off, their use of (as SPLC implies) "biased" experts differs from the gay movement's own activists and researchers how?

 Second, the final sentence of the above quote shows a complete disregard for and misunderstanding of Christian culture. Pastors need to be transformed into opposing the gay movement? 2000 years of Christian (and Jewish before that) tradition has established that homosexuality is immoral. Pastors who teach that are doing their job, from a doctrinal standpoint. To suggest the FRC is corrupting religion by emphasizing traditional values and rejecting the gay movement is misleading, at best, intentional outright lies at worst. http://www.splcenter.org/get-informed/intelligence-files/groups/family-research-council In Its Own Words
“Gaining access to children has been a long-term goal of the homosexual movement.” — Robert Knight, FRC director of cultural studies, and Frank York, 1999
Since the SPLC offers no context for this quote, I will take it at face value and not read anything further (namely the idea homosexuals are recruiting young men/children for gay activities, as stated later, we'll get to that). http://legiscan.com/gaits/text/74798
State of California, Senate Bill 48 (SB48) 2011

"This bill would require instruction in social sciences to also include a study of the role and contributions of (snipped out list of ethnic groups), lesbian, gay, bisexual, and transgender Americans, and other ethnic and cultural groups, to the development of California and the United States."
http://www.leginfo.ca.gov/pub/11-12/bill/asm/ab_1851-1900/ab_1856_bill_20120222_introduced.pdf
State of California, Assembly Bill 1856 (AB1856) 2012

Regarding providers of foster care for orphaned children:

"The administrator certification programs (Administrator, as in the head of household in a "group home" where orphaned children are cared for) shall require a minimum of 40 hours of classroom instruction that provides training on a uniform core of knowledge in each of the following areas: (snipped out irrelevant points) (I) Instruction on cultural competency and sensitivity relating to, and best practices for, providing adequate care to lesbian, gay, bisexual, and transgender youth in out-of-home care."
It is PLAINLY obvious that the "homosexual movement" is demanding, through backroom legislation, access to children. Perhaps, and probably, not to involve them in so called "gay activities", especially against their consent, but most certainly to indoctrinate them into a mandated sense of "tolerance".

http://www.splcenter.org/get-informed/intelligence-files/groups/family-research-council
“[Homosexuality] … embodies a deep-seated hatred against true religion.” — Steven Schwalm, FRC senior writer and analyst, in “Desecrating Corpus Christi,” 1999
“We can learn to ignore the bullshit in the Bible about gay people – the same way we have learned to ignore the bullshit in the Bible about shellfish, about slavery, about dinner, about farming, about menstruation, about virginity, about masturbation. We ignore bullshit in the Bible about all sorts of things.” - Dan Savage, gay advocate and blogger.

"If not for the Mormon church and its campaign of hatred, California’s Proposition 8 — which would take away the right of men to marry men, and women to marry women — wouldn’t even be on the ballot. And without the millions of dollars it guilted and coerced its members to donate, the proposition most likely would not have passed on Nov. 4. I blame it all on the Mormons." - Jodi Mardesich, activist and avowed bisexual.

"When gay marriage is legal everywhere, the opponents will be revealed for carrying water for a larger kind of orthodoxy. Their church is opposed to same-sex marriage because same-sex marriage means diversity, and diversity means peaceful interactions between members of different groups and religions, and peaceful interactions means fears and prejudices are diminished, and the diminishing means those churches' cartel in the religion business is jeopardized." - Keith Olbermann, Television host and political commentator.

There is plenty of anti-religious sentiment and speech among the gay movement. Pointing this out is a statement of fact, not necessarily hate speech.

http://www.splcenter.org/get-informed/intelligence-files/groups/family-research-council
“One of the primary goals of the homosexual rights movement is to abolish all age of consent laws and to eventually recognize pedophiles as the ‘prophets' of a new sexual order.” -1999 FRC pamphlet, Homosexual Activists Work to Normalize Sex with Boys.
As the SPLC page goes on to note later, this specific document from the FMC is no longer available, but I will grant the SPLC the benefit of doubt and assume they have accurately presented this quote.

The following two quotes relate to the same issue, I present them and then address all three.

http://www.splcenter.org/get-informed/intelligence-files/groups/family-research-council
“[T]he evidence indicates that disproportionate numbers of gay men seek adolescent males or boys as sexual partners.” — Timothy Dailey, senior research fellow, “Homosexuality and Child Sexual Abuse,” 2002

“While activists like to claim that pedophilia is a completely distinct orientation from homosexuality, evidence shows a disproportionate overlap between the two. … It is a homosexual problem.” — FRC President Tony Perkins, FRC website, 2010
http://nambla.org/welcome.html
"WELCOME! The North American Man/Boy Love Association (NAMBLA) was formed in 1978. It was inspired by the success of a campaign based in Boston's gay community to defend against a local witchhunt. NAMBLA's goal is to end the extreme oppression of men and boys in mutually consensual relationships by:

building understanding and support for such relationships;

educating the general public on the benevolent nature of man/boy love;

cooperating with lesbian, gay, feminist, and other liberation movements;

supporting the liberation of persons of all ages from sexual prejudice and oppression.

Our membership is open to everyone sympathetic to man/boy love and personal freedom. NAMBLA calls for the empowerment of youth in all areas, not just the sexual."
They do go on to state that they advocate breaking no laws, but... (same link)
NAMBLA does not provide encouragement, referrals or assistance for people seeking sexual contacts. NAMBLA does not engage in any activities that violate the law, nor do we advocate that anyone else should do so.

We call for fundamental reform of the laws regarding relations between youths and adults.
Their own words, their own website. Pretty damning evidence. Admission of the desire to change the laws regarding relations, "not just sexual" but including those, between adults and children, and an explicit admission of their foundation based in the gay community of Boston! Sick. Just sick.

Further, Kevin Jennings, Founder of the Gay Lesbian & Straight Education Network (glsen.org)and appointee to the US Department of Education under President Obama, is not only on record teaching "fisting" (google it if you must, but be forewarned, not work or kid safe) to minors, but evidence strongly suggests he has at least once condoned, failed to report and possibly enabled the statutory rape of a minor by a gay adult.

The following link is to a rather in depth report on that evidence by Grove City College Professor of Psychology Warren Throckmorton:

http://wthrockmorton.com/2009/06/02/kevin-jennings-appointed-to-department-of-education-post/

While it is perhaps unfair of the FRC to make statements such as "One of the primary goals of the homosexual rights movement", the evidence exists that there are elements in the homosexual movement to which these are goals. NAMBLA itself, as I pointed out, points to its origin in the gay rights movement.

SO...

The SPLC and the gay activists can rant and rave all they wish about FRC's "hate speech", but the truth is, it is not hate speech at all. It is the truth, albeit with a certain point of view attached, but that happens with any political organization. Facts are facts though, however they are presented. The FRC is being attacked for speaking the truth. Chick-Fil-A's president is attacked for speaking his mind, outside of his role in the company and distinct from any company policies or practices. This isn't about honest discourse. It's not about tolerance. It is about 100% non-negotiable compliance to the gay agenda. Resistance will not be tolerated.