The short answer : because Buu was more powerful than the dragon.
Statement : The dragons have the power to do things that the rulers of the universe cannot. Where does this information come from ? As you stated, the power of the dragon depends of the power of its maker. The first dragon we meet can only resurrect one person per wish, whereas the latest can resurrect the entire Earth population. This is because the Namekians perfected their art of dragon creation. And probably because they grow more powerful with time.
Buu is an extremely powerful being whose powers match the Supreme Kais'. He can instantaneously tranform people into candies. He can even transform Vegeto, an also extremely powerful being, into chocolate. He can regenerate at a rate which make fighting against him nearly impossible. Remember that Buu ate one of the Kai...
The guy is tough, that's it.
EDIT : You did not define "Ruler of the Universe" in your question. To me, Supreme Kai and Ruler of the Universe aren't the same thing. The Kais are more like a police. If there was really a "Ruler of the Universe" in Dragon Ball, I think it would be the guy who ruled heaven.
Regarding your second comment, we can only guess than resurrecting the most powerful saiyans requires as much power as resurrecting the most average human, not more. In the series, resurrecting merely means "bringing back the soul from heaven".