No, people who make a difference are not always popular. They often are not. They do not like the status quo, and most people will hold onto the status quo with all of their energy. Making a difference is hard, often thankless work.
Of course people who make a difference are not always popular. In order to make a difference, you typically have to be somewhat aggressive or assertive. This can make you unpopular. You have to try to upset the status quo. This can make you unpopular as well. If you are in high school, people might think you're some kind of weirdo if you are trying hard to improve things. So no, people who make a difference are not always popular.
As long as you're not looking for people to make a large-scale difference, then yes, ordinary people can make a difference. For example, an ex-student of mine who overcame cancer and a very impoverished background comes back to her school every so often to talk to kids from the same migrant worker, poor background about going to college and achieving. She's not going to end poverty, but she may impact the lives of a few of those kids and that's important.
1) By popular, I assume you mean liked or highly regarded. There are leaders in history who have made a huge difference in our world but they were not popular. For example, Hitler made an difference - he created a war in which the majority of the free world participated.
2) Ordinary people make differences all of the time. Sully, the airline pilot who saved all of those lives, is a great example.