Regardless of the point-by-point response, I think the general idea is that women have historically been disadvantaged in education, so Title IX _de facto_ helps alleviate that problem, although there are obvious negative externalities that result from a blanket application. I do think that a couple of your (x) arguments assume malice where there likely is none, but I've responded point-by-point below.
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(1) This is the question at the heart of any sort of redistributive action government takes -- it seems like we, as a society, have decided that it (or things analogous to it) are ok, at least some of the time.
(2) I would hope not! That's certainly not how I've thought of it, as a young male.
(3) Presumably when the indicators of discrimination are no longer so blindingly obvious (ranging from unequal pay to glass ceilings). I don't, however, suspect that it's going to be that simple. I think that a lot of the biases fueling the problem are culturally inherent, and can't be resolved just with legislation. Although the idea behind Title IX seems like a step in the right direction.
(4) By participation in a democratic society. Great question though! I'd like to think that it isn't zero sum.
(5) First of all, I don't think that we necessarily have to do one at the expense of the other. I also don't think that there's any sort of fairness mechanism by which we get to make things universally better for everyone all at once. We work with the Congress we've got, and the Administration we've got, and the Supreme Court we've got (x50 for the state level!) to do the best we can. That being said, I think it's ok to prioritize some problems over others, and problems affecting ~50% of the population are generally worthy of increased scrutiny IMO.