I think the answer is no, but I want to confirm.

Can you use a Protector when someone uses an ablity. For example when the text says something like 'target ally or hero'?

no

Protector can only be used during combat at a particular part of the Attacking process. Head over to ude.com/wow and check out the comprehensive rules document. Its not the easiest read but its the best place to figure stuff out.