Since they dont die from living in this stuff, I guess it does stand to reason that the crocs (or gators) themselves have some built-in protection from it.
Komodo dragons must have similar properties as well. Their mouth and bites are considered the dirtiest wounds you can get.
Or the pathogens just don't target crocs/gators. Many (most?) pathogens are pretty specific in what host organisms they will cause problems in. And most bacteria and virii don't cause disease anyway, so simply having a lot of them around is not a cause for alarm in itself. Heck, I read the other day in Answers magazine that there are 10 bacteria in your body for every one of "your" body cells! Biologically speaking, you're a big mass of bacteria!