I think a big difference between songs in commercials and movies is that commercials are only trying to sell something. Basically they are using music and the musician makes money and whoever is selling something makes money...it's all about money. But movies (the good ones) aren't trying to sell something, they are trying to tell a story. Maybe I'm too naive about movies and they are just about money, but I hope not.
A good test is to ask "Would I let them use my song if I wasn't getting paid and I wouldn't get any more record sales because of it?" If the answer is yes, I don't see a problem.