Two reasons. First, it's the office that's immune, not the person. If you prosecute a person for something they did "as president" then you're prosecuting the office. Second, it's not to be fair to the person. It's to protect the government from collapsing. People forget that happens all the time, often due to ineffective executive leadership. Look at Haiti, etc. So, I think it's true that Presidents will get away with a few things here and there that they shouldn't, Congress can still impeach and remove them. If Congress is on-board with what the President is doing, then that's a decent safeguard that "at least whatever the President is doing isn't going to destroy the country."