He was the first captain out there; they hadn't learned to fight yet.
This makes the most sense to me. I like to think that Archer getting his ass so thoroughly trounced is part of what led to Starfleet expanding its physical training programmes to include stuff like Sisko's wrestling team.
That and the integration of MACO, I suppose.
I was actually poking fun at the "he was the first captain!" excuse everyone else uses for Archer's other faults.