It's pretty much part of their culture, so if you're having that big of an issue about it, stop watching Japanese shows. Heck, cross-dressing has been part of Japan even in the 1600's since Kabuki shows had cross-dressing men (Onnagata) since women were at one point banned in performing. Even up to now, Japanese theaters feature women doing male-roles and vice-versa.
So stop waving your mental-incapacity to comprehend why cross-dressing exists in Japan, since not everything in the world is tailor-made for you. You're the one watching the show, it's not like they're forcing you to watch it, if you don't like it, nobody cares because it's not gonna stop.