I don't think they are being targeted any more than any other group. When there is a private charity organization that doesn't allow Jews, for example, they would also not exempt from taxes: they wouldn't be exempt because they discriminate. Your problem is that you think gays should be discriminated against; however, the majority of people in the nation do not agree with you. Too bad for you. For example, the KKK, no matter how much 'charity' work they might do, would not be exempt from taxes because they discriminate. Maybe you can wrap your mind around that.
The Catholic church will not allow same sex couples to marry in their temples. It won't change. In your book this is discrimination; isn't it? Will you compare the Catholic church with the KKK and antijew groups? Of course, many will. This is coming soon.
It's already happening on small scale:
Washington Florist Sued For Refusing to Provide Flowers For Same-Sex Wedding - ABC News
So taxpayers who don't agree with the government must be discriminated... in the name of non-discrimination.
PS: I'm for gay marriage. But it's becoming clearer and clearer that there is a "gay agenda". A political and ideological agenda. And gay marriage is only the first step.