What is the difference between a nice jew that waers a Kippa to a nice jew that doesn’t wear a Kippa? I know that shows they are religious but is there a deeper reason?

Wearing a Kippa indicates 1. awareness that there is a G-d above 2. a sense of modesty and self deprication 3. an identification with the Jewish people. Many people wear a Kippa with one or another of the above understandings, some have no understanding at all. Like any particular act, it is a small part of a person's general makeup and in itself cannot mean a person is superior to anyone else. To the extent that a person has the awareness I mentioned, the Kippa makes him different. On the other hand, without any awareness the Kippa is an empty symbol, and people may see it as a form of hypocrisy. Don't be against the Kippa, but try to ensure that it represents something more than just a colorful cloth circle on the head.