I think that if enough exit nodes would be owned by let's say government agencies they would be able to correlate requested domains with actual requester IP.

We all should run a Tor node then to outnumber the bad guys

In addition to the traffic analysis mentioned in another reply, there are ways data can be leaked from Tor. One example from the crime documentary "Hunting Warhead": a white hat hacker managed to locate a darknet server running a forum software by setting his avatar image to a file hosted on a domain he controlled. The forum software retrieved the age via a regular internet route, exposing the actual host IP.

For maximum privacy, Tor should be used with software designed for Tor from the start.

Not sure I would call Tor "perfect", but it's certainly very useful for some use-cases.