Stuxnet doesn't act like a criminal worm. It doesn't spread indiscriminately. It doesn't steal credit card information or account login credentials. It doesn't herd infected computers into a botnet. It uses multiple zero-day vulnerabilities. A criminal group would be smarter to create different worm variants and use one in each. Stuxnet performs sabotage. It doesn't threaten sabotage, like a criminal organization intent on extortion might.
Stuxnet was expensive to create. Estimates are that it took 8 to 10 people six months to write. There's also the lab setup--surely any organization that goes to all this trouble would test the thing before releasing it--and the intelligence gathering to know exactly how to target it. Additionally, zero-day exploits are valuable. They're hard to find, and they can only be used once. Whoever wrote Stuxnet was willing to spend a lot of money to ensure that whatever job it was intended to do would be done.
None of this points to the Bushehr nuclear power plant in Iran, though. Best I can tell, this rumor was started by Ralph Lagner, a security researcher from Germany. He labeled his theory "highly speculative," and based it primarily on the facts that Iran had an usually high number of infections (the rumor that it had the most infections of any country seems not to be true), that the Bushehr nuclear plant is a juicy target, and that some of the other countries with high infection rates--India, Indonesia, and Pakistan--are countries where the same Russian contractor involved in Bushehr is also involved. This rumor moved into the computer press and then into the mainstream press, where it became the accepted story, without any of the original caveats.Schneier also looks at strings found in the Stuxnet worm's code, some of which suggest, somewhat tenuously, either that it's of Israeli origin or that the authors wish to give the impression that it is.
Basically, all that's definitely known is that Stuxnet was elaborately expensive to create (containing not only zero-day vulnerabilities but stolen driver certificates) and was designed to attack Siemens plant control computers. It also has been around for a while, possibly having gone undetected for a year, and has updated itself remotely during that time.
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