The crown is the very end of the barrel at the muzzle. It basically is a carefully machined angled surface that insures that the pellet leaves the muzzle consistently every time. If there is a problem with it, accuracy and consistency will suffer.
This is why we usulally clean from the breech end, and it is best done by removing the bolt - then you have a clear access all the way through your rifle for cleaning. An alternative is to use weedwacker line (which won't damage the crown) and pull patches through. The best way is with a crown saver type cleaner like Mac1 sells.
If you were carefull and only did the one pass from the muzzle to get the pellets out, you would not have hurt the crown, so don't worry about it. But repeated stroking of a a rod against the crown will damage it.