I am not that well versed in trans-atmospheric travel, but this is how I understand it:
Re-entry isn't at the same speed that it (or much else) travels is the atmosphere.
During lauch, the shuttle accelerates gradually, not reaching its highest speed until it has already passed beyond the atmosphere. In re-entry, although not travelling as fast as normal orbit, the shuttle is moving at around 15,000 mph...which is faster than it moves in the atmosphere during launch.
I haven't read up on this but like I said, this is how I have always understood it.