Absolutely; and it's only a matter of time until they do. Note that this is a problem only on some of the newer devices. I have the original Droid, which is well-compromised at this point. I haven't rooted mine yet, but only because I haven't come across anything I want to do that calls for it. Yet.

I seem to recall there was even a recent court ruling to the effect that it is not illegal to root, jailbreak, or otherwise crack a smartphone's software, so the only real risk is damaging your phone in a way that the carrier will refuse to repair.