Never use a crop as punishment. Only use it to ask for a little more energy when you are riding. If you use it for punishment the horse may thing he is being punished when you tap him to, for example, canter. Then he might think he is being punished for cantering.
I've never had a horse become afraid of a tool just because I've used it to thwart nasty behavior; granted I don't "just" use it to discipline the horse...when I use it it is used to encourage movement of some form; so if he's trying to kick me, I'm going to move his hips, if he's trying to bite me, I'm going to move his shoulder, or push his entire body away from me.
In a case like this, my crop, carrot stick, whatever, would be used to strongly encourage the horse to MOVE out of my space NOW!!!! BUT, I have used my elbow, or crop, or whatever to get a horse to get his face out of my space, and again, they don't become fearful of it...I think it's in the way the equipement is used every single second one is with a horse, and whether there is any release to that pressure...yes, thwacking a horse repeatedly for nipping or kicking, will wind up being counterproductive in the sense that all you're doing is hitting him; ie there's no purpose behind it, but if you're using your tools to achieve a purpose there should be no reason for the horse to confuse the use of it.