Phiteros' answer states the fact that plutonium is in scarce supply and PearsonArtPhoto's answer points out that Juno's mission profile allows it to use solar panels. These issues are legitimate and (the scarcity one anyway) somewhat overriding of other issues. Nonetheless, I wish to bring up something else: Public relations and politics.
In the opinion of some people, using radioactive materials in a device that could explode is too risky. Thus, every time NASA uses RTG's on a mission, there are protests about the risk of exposing the public to radiation should there be a launch accident. This brings about negative news reports about the agency. It also likely brings some pressure on NASA from some politicians to find another way to power its spacecraft.
Note: I'm not agreeing with the position that RTG's are too dangerous to launch into space, just pointing it out.