If anybody failed to get the ridiculousness of my last statement, I'm basically saying that boycotting Chick-fil-A because Dan Cathy supports anti-gay organizations is akin to not going to see a Disney movie because Walt Disney was anti-semitic. If the standard of acceptability from my business is perfection, then we won't be shopping anywhere.
That also means that just because I shop at a place, watch a movie, or eat food somewhere, I am not supporting everything that company's executives support. It's a stupid a concept as saying voting for a presidential candidate means you support everything that candidate stands for. Nobody's perfect, so I just have to make the best with what's available.
I think a key difference is that Chick-fil-A are quite publicly supporting Dan Cathy's stance though. Ever visited Chick-fil-A's Facebook page? There are only statements of support for their noble crusade against the filthy homosexuals. Statements of disagreement, even friendly, rational, or reasonably worded ones, are removed immediately.
Contrast that to Disney, who (AFAIK) have never said, "Yes, we as a corporation support our founder's anti-semitism."
Yes, companies are probably spending their money on causes I disagree with all the time. For all I know, the manufacturer of the keyboard I'm tapping away on right now is secretly stealing fissile materials from abandoned power plants and selling the stuff to terrorists. But they're not making a public statement out of it.
Contrast that to how Chick-fil-A have basically drawn a line in the sand. "This is what we believe in. So are you with us or against us?"