For starters, once again, Fedor fought a larger opponent. Arlovski was both taller, had longer reach, and was heavier.
Secondly - I can't find the video, but there was a video where they slow motioned almost all the exchanges. When I first watched the fight, I thought Arlovski was hitting Fedor a lot, however, in the slowmo, it was obvious that 90%+ of Arlovskis punches did not hit. Fedor rolled with them and they hit his shoulders. Just look at Arlovskis best punch - the right hand at 3.48 in the video that really looked like it hit Fedor hard - it actually did not even touch him. Just slow the video down, and you will see that Fedor rolls with the punch.