I think that is something you are going to have to answer for yourself. It could be a combination of internalized misogyny and poor writing of female characters. If you can't connect with them in some way, that makes it harder to like them.

Personally, I when I was younger I was definitely a tomboy and considered my more masculine qualities to be better than my feminine ones. At times in my life that's changed and, now that I think of it, I enjoyed those times of embracing my feminine side. Maybe you have a strong masculine side to your personality that you are more comfortable with. It's ok, but just keep in mind that you should still give female protagonists a chance in the future. You may not feel like this forever.