Oh, I don't know that I made this entirely clear, but I'm not saying that this is MS's FAULT necessarily. I agree, if Amazon or Google had purchased Github, it would have been the same thing.
I think the slight difference is that MS does have a history of shitting all over open-source software (Ballmer famously said Linux was cancer years ago). While I'm aware that companies change people all the time, it's unsurprising that some people get a little bit uneasy about them owning the largest distributor of open-source.