Certainly I've felt unsure, especially when I was first starting out, didn't have a ton of experience or confidence in my judgments, and still felt like a fraud putting myself out there as a "trainer." I don't know if that's the type of uncertainty you meant to ask about... but anyway, I had it, and lots of it!
I still think a healthy dose of caution, humility, and self-questioning is important. People who have total blithe confidence that they're always right don't tend to have the most accurate judgment about that or much else, in my experience.
But if you're doing it right, you shouldn't be putting the dog in an unsafe situation, either for that dog or for anyone else. Controlled exposure is key. I try very hard not to subject a dog to more than it can handle, and to have safeguards in place to cut off any trouble immediately if it arises.
Beyond that I'm not sure how to answer your original question. In general, aggression cases are not the sort of thing I feel particularly comfortable giving advice about over the Internet, particularly since I get the sense from some of your other posts that there are a lot of other things going on here.
ARCHMX TDCH Pongu the Insane, CD-C, RE, RL1X6, RL2X5, RL3X2 (GSD mix, b. Apr 2010)
Crookytail the Tigerwuff, RL1, ITD (Akita mix, b. Jan 2011)