Omg, you guys. I was a bad mommy once too, but then I got over it. *rolls eyes*
Kick yourself quickly (and hard), make sure the dog's not
actually hurt (quick injury check, and/or 5 second apology), tell the dog "Yep, you're okay" (in dog language) and the dog will get over it too. Obviously you didn't hurt your dog, and his fear of whatever happened to him in his past could be easily reinforced by how you react now.
Scruffing is a natural instinct (scruffing is what it's called when the mother carries her young around by the scruff of the neck), and should not be a source of emotional distress. Unless of course injury has occured, in which case there could still be something which could cause physical pain when touching the area. If no physical pain is present, there is no reason why your dog should fear this, and it's our jobs as pack leaders (in dog psychology, not human), to remove the fear (as mummummum knows all too well).
Honestly... you guys...
