The ACLU historically has not always opposed religious freedom. The organization did support RFRA in 1993, after all. It has long held itself out as a protector of individual rights, and has done that in a number of areas. However, it continues its now sad and all-too-familiar decline regarding First Amendment Free Exercise rights (and Establishment Clause jurisprudence).
The latest marker of this decline is the organization's opposition to proposed federal protections (the First Amendment Defense Act or "FADA") ensuring the government can't discriminate against people because they believe marriage is between a man and a woman. Yes, the ACLU is opposing a law protecting individuals from the government -- a law which protects both religious and nonreligious people in exercising their beliefs. How did we get here?
While I don't know all the ins-and-outs of the organization's internal decision-making, it appears simply to have prioritized sexual liberty (and the individuals rights protections it sees as advancing this liberty) over other rights, including First Amendment religious protections. This is the reason that, in the interval since 1993, the ACLU has developed its concerns about RFRA. Nothing must interfere with sexual liberty, religious or otherwise.
The problem (among others) with this approach is contained in a simple question: What are the limits of this sexual liberty? By holding up such a loosely contoured and ill-defined right above all others, the ACLU (and others with the same aim) ultimately cannot say what these rights to sexual liberty they are protecting will look like in the long term. While the ability to "define and express" one's "identity" (as the Supreme Court explained in creating a right to same-sex marriage) looks like one thing today, what will it look like tomorrow?
I wish I could say otherwise, but the ACLU is playing with fire as it loses the moorings on which it is able to secure any protection of any constitutional rights. When any rights develop such a nebulous character, they threaten the foundations of other constitutional and civil rights -- and ultimately the very foundations and systems supporting these rights. Some of the first casualties are RFRA and First Amendment Free Exercise rights. Now it appears FADA will be thrashed next. And it's not the last; there will be others. The philosophical assumptions adopted by the ACLU demand further application.
This is why my heart isn't lifted by the ACLU's promises regarding FADA:
"Despite the claims of some marriage equality opponents, the First Amendment already protects the rights of churches and clergy to decide which unions to solemnize within their faith traditions. Since the founding of our country, no church has been forced to marry any couple in violation of its religious doctrine and that will not change now that same-sex couples can marry. And, the ACLU would be the first to rise in defense of these religious institutions if government ever tried to do that."
Perhaps so, for now. But such promises can't be sustained over the long term. The methodology and philosophy adopted (to my dismay) by the ACLU demands it.