I just started rolling FIM out for a PCI requirement and noticed this issue as well....We have some folders in our environment with special config files we don't want touched, this same folder has app logs that are constantly changing.
It would be nice if we could configure "exclusions". Right now we're looking at making 20 individual file monitors...making 2-3 exclusion would be easier, or having the ability to ignore extensions.....like exclude " *.log " in the folder.