But the simple fact is that you should have to repeatedly pummel them. Given enough time (and population - tiny islands are probably exempt) it's virtually inevitable that a colonial society divided from their motherland by 3,000km of ocean, no matter how nice the motherland is to them, is eventually going to start identifying not as 'British' but as 'Americans' or whatever, and start wondering why they should have to listen to the motherland at all.
Yes, I agree that (like many of the new mechanics introduced in EUIV's lifespan thus far) the colonial nation mechanic is vestigial and dramatically lacking. There should be a way to peacefully give colonial nations their independence but still keep them in your orbit, like the British nominal control over Canada and New Zealand and suchlike... But as it stands, I think this system is dramatically better than the old one. Colonies should revolt. Prior to this change dominating the Americas wasn't a simple side-game, it was a very easy process of boost tariffs to 75-85% and forget. Now at least you have to make considerations and think about things.