We see someone’s POV going through a transporter, you just see where you are, sparkles, and now you’re somewhere else. The unease probably comes from the uncertainty. The mere fact we can’t ascertain what really happens in a transporter to your consciousness is very suspect in a universe like Star Trek where we find science babble for everything.
Though, think of it for a moment. Your atoms are being torn apart and the structure is being rebuilt somewhere else. That totally just sounds like you die. I wouldn’t want to go in there either.