First, let me start by pointing that he is by far the most powerful God in the universe. His power dworfs every other "Ki" that we ever see.
Now then, you may not think it, but Kaioshin(the real name of "Supreme Ki")is a real heavy hitter. He states as they fly "Each Kaioshin is powerful enough to kill the one you call Freezer with a single blast".
You may recall that and say "Freezer? So what? Goku of Vegeta could kill him with a flick of their finger! He's a wimp!".
What you have to remember is that the Z senshi are literally freaks of nature when it comes to their power. In the grand scheme of things, Freezer ranks right up there with Gohan & Goku & Vegeta & Cell (so on) as the strongest people in the universe. As a matter of fact, before the wole Namek thing happened, Freezer was the most powerful non-God being in the DB/Z universe.
So the fact that Kaioshin can kill Freezer with a single blast says a hell of a lot about his power, and shows that Kaioshin is freaking strong.
...so if Kaioshin's so strong, why is he scared of Buu? Because back when Bibidi first created Buu, all 4 Kaioshins gathered together to stop him. Buu killed 2, and absorbed 1. While this was going on, the final one used magic to imprision Buu.
Buu was able to take out three of the most powerful Gods in the universe. Now there is only one left, and the creature that did all that is about to be relieced again.
Yes he freaks out, because he knows Buu can kill him easily. To his knowledge, no one else alive has a better chance against Buu than he does(he had no idea what kind of power the Saya-jins had).
So yes, Kaioshin is powerful, but unlike other characters, he recognizes his limits.
Yes, Kaioshin is afraid of Buu, but he'd be a fool not to be.