Yeah, the myth about the hair color and intelligence should be killed with fire. I have a medical degree and I finished it with best possible grades, yet I still have to prove myself every day to all kinds of assholes that I meet for the first time.
I bet there were some weirdos about the whole blonde thing, but I think the main point about the whole "beauty pageant" was that they picked blonde, yet the ME1 and ME2 default Shepard had red hair, so it did look kind of unnecessary. It's the context that rubs people the wrong way, I guess. First Bioware realized that FemShep is popular, then they held a beauty pageant (!!) and redesign her from scratch, with blonde hair and lots of make up. So it's not about blonde people per se, but about Bioware's track record. Luckily, she stayed mostly intact, the only thing that they managed to screw up was that god awful run when in casual clothes, but that was balanced nicely with her gorilla run & shitty dancing, so no harm there.