You've experienced trauma and it's perfectly natural to be averse to something that was involved in that trauma. What you need to understand is that trauma was tied to the person and not the skirt. You can do something called "exposure therapy". Basically what you do is you keep wearing the skirt and soon your brain will lose the association with being assaulted and you will gradually become more comfortable.
I genuinely believe that what happened to you was an isolated incident and won't happen again and that you should continue wearing skirts.