I don't have sources to cite, so take it however you will, but when I looked into this a few years ago, I found that the majority of fast food companies support more conservative than liberal organizations and with their political spending.
So while Chick-Fil-A got a lot of public attention… if you are ONLY boycotting them and not all the others, it is because you haven't looked into who is doing what. This is not a criticism, just something to hopefully prod more into discussing the issue on a larger scale.
Everything is a choice. And things are very interconnected. It's difficult to decide where to draw lines. For example, I boycott Harry Potter these days, but I have a bit more trouble boycotting Neil Gaiman. Others I avoid and yet others I minimize or don't avoid. Purity tests are a choice, but they are weakened by ignorance about who all has done what.
By existing in modern society, we purchase most things that eventually are owned/created/provided by large corporations, most of which work against human rights.
So my point is: Pick and choose where your lines are, but if you do truly care, then you really have a lot of research to do or else your choices end up doing most of the harm you try to avoid.
And for the slower on the uptake: I am not arguing against boycotting Chick-Fil-A; rather, encouraging education as they are neither the only nor worst offender.