They quite are. The number of goals is almost identical, and Messi usually makes like 5 assists more than Ronaldo for season, so it is very close.
Ronaldo has quite better movement in the box, that is why he is always in good positions to score a tap in. And as you said, pens and headers. Messi is better at other stuff but when you add all of them, they are at the same level. The difference doesn't come from their end product but from their general gameplay, when Messi wins. Ronaldo is fantastic in a counter attacking team (as we have seen for both United and Madrid), but Messi has as good general gameplay as pretty much anyone in the last 20 years or so (well, Xavi and a few might have been better at it). If the opponent shut downs Madrid and starve the service they can give to Ronaldo, he will likely have an average game. If the same happens to Messi, he will come deep and influence the game, putting his teammates in good position. He is just the better player.
There would have been a good discussion if Messi's end product will be quite worse than Ronaldo's, and then it will be more difficult to see if Ronaldo with 60 goals and good gameplay is better than Messi with 40 goals and awesome gameplay. But when the end product is identical, then it becomes Ronaldo with 60 goals and good gameplay or Messi with 60 goals and awesome gameplay. Not that difficult to come to the conclusion.
