Your co-worker does not owe it to you (no, really) to put down the seat because he has a penis. You are not sleeping with him...and it's really not that big of a deal to flip the lid down prior to sitting. I'm a female, I know. Going to the boss over this, really?

That being said...(and as others have mentioned) if the toilet has a lid, it should always be in the down position prior to flushing...because, ew. I saw that episode of Myth Busters.

Maybe for the socks suggest a small dirty clothes bin? Definitely get some sort of air deodorizer...no bathroom should be without that and a can of Lysol.

And above all...GET OVER YOURSELF. I doubt you're a "superstar" and he "resents you" quite as much as you think.