Not sure about the transphobia, but it is definitely on the sexist side. The whole premise starts out with dumb hot girl being hounded by smart inept nerd and friends. This of course continues in various ways and lets not forget Howard.
I do wonder though, this was pretty much the point of the comedy. Shining a light on stuff like that.
Most older shows don't perform well with more current ideals in mind. Media should be viewed in the context of its time and people were generally less aware of how harmful certain portrayals could be.