If you have a problem with music being used in commercials, then you really shouldn't be listening to music from professional recording artists in the first place. When you bought their CDs, you were supporting a commercial company who paid the Flaming Lips for the rights to distribute their song. Not much different from the TV ads, really. You can probably find some high school garage bands who aren't in it for the money.
I suppose if you have some strong hatred of Mitsubishi cars, or if the Lips became famous by writing songs about how everyone should take the bus or ride bikes (they didn't, did they? I haven't heard their first albums), those would be good reasons to be upset about the commercial. Or if they decided that all of their future songs will be bouncy songs about driving along in a Mitsubishi, that might be a good reason to be upset too...