Yeah, it's all from the same origin. The implication being that the one penetrating is "the man" and the one being penetrated is "the woman." The other part of the implication being to fuck someone is good and powerful and dominating and being fucked is bad and immaculating and submissive.
If that sounds like I'm adding my own words and meaning to a simple phrase, think about what is actually being said when you say "you're getting fucked by Microsoft." What, you don't want to get fucked? Why? Sex is supposed to be a positive thing two people can do together. Unless the one "getting fucked" doesn't want to and now we're not talking about fucking, we're talking about using violent rape as an analogy for what a software company is doing to its userbase and that's just...kind of fucked up. I shouldn't have to explain why, right?
Anyway, no, I don't get mad whenever I hear a phrase that stems from heteronormative ideas of sex. I don't assume the person saying it is homophobic or an idiot, they probably just don't know. But a friend once educated me on the subject, I thought about it, and I agree. So now I avoid using phrases like that, and when someone openly questions it like you have, cool, I'll stop and talk about it.