I tried public transportation the second week I had arrived. It was a scary process. The reasoning was because everything was in a different language. Japanese use 3 different ways of communicating: hiragana, katakana and kanji. When you order your ticket you have to know where your going, how many stops to get there. And when to get off. And how much the ticket is. You could be heading towards Osaka but end up in a completely different area.
Another scary process would be to ask for help but you only speak English and the station attendant speaks only Japanese. When me and a friend wanted to go to Osaka, we got completely lost and a stations that was three floors and no one could help us. We were stuck wandering for an hour till one of our friends found us. But even though these sort of situations can be a truly scary situation. The positives are that you are learning to adapt to an experience completely new. I also learned a lot about a culture that truly interests me.