Separate the writer's choices from the characters' motivation.
How many of these things happened DIRECTLY because Steve or Tony have or had issues with women and not just because the writers aren't utilizing the characters? I think most of these things are really more the latter.
The closest thing I can think of is Tony constantly going over Carol's head when he put her in charge of the Mighty Avengers.
But I ask this:
Was this specifically because she was a woman?
Or was this because Tony's just an obsessive control freak who can't let go? (IE - would he have done that to pretty much anyone?)
If he really had a problem with women, why would he put her in charge anyway?