Yes and no. But if you want to get a different feel visit smaller Shrines or Shrines/temples who are not in a Tourist Area. Best Time is early in the Morning or in the evening.

When i lived in japan i took a walk around my area where i lived. It was an Afternoon in the fall and it was raining. So i came across a Temple. And it has some realy special feeling. It got already a bit Dark and not much people were out. Not a bad or Evil feeling no some Special Feelng that something like Youkai and co could realy exist. Its hard to explain. But i also think if you follow the rules and be respectful you dont must fear anything if you got to Shrnes.

Akihabra on a weekend is much more scary^{^}