I think I would be strangely flattered by that. I mean they must really think he is awesome to go out of their way to actually find someone who only SOUNDS like him. Pissed off, sure, but also kind of flattered 
Well, the problem with that particular situation was that the company in question aproached Tom Waits to do the add, and when he flat out refused, they went over his head and found an imitator. It was pretty understandable why he would be mad.
The real question here should be whether or not a certain song being used in a commercial lowers its emotional impact. Of course, artists are people who have to pay bills, and commercials also give them exposure. Commercials have been playing more inovative and indie music than any radio station in the country has been for years.
And sometimes they get to have fun with it too. The Shins license out songs in a subversive way, like "New Slang" ("The dirt in your fries", "Bleed into their buns") which was licensed to McDonalds for an ad, or "Young Pilgrims" ("I know there is this side of me that/Wants to grab the yoke from the pilot and just/Fly the whole mess into the sea.") which was licensed to an airline.
But what happens to the emotional connection between artist and listener when someone's favorite song is used to hawk clock radios or something? It cheapens the entire thing.
I'm not going to hold it against any artist that does license their songs out, but I'm not going to pretend I feel the same way about the song afterwards either.