Put yourself in your opponent's shoes. How would you feel if you were Black and he was White and he still managed to win although you have more material? I get fed up already in plenty of games when my opponents refuse to resign when I am clearly winning but run out of time.
Winning on time in situations like this is to me poor sportsmanship, and doesn't reflect how the winner actually plays. If anything, I think it's insulting and rude.
This doesn't apply though when both sides have comparable amounts of material. But in games like the one mentioned above, it most certainly does apply as bad manners.
Fair means the rules are applied the same way to all involved. Therefore, if one person runs out of time, it is "fair" to accept the win. You dont need to feel guilty about winning on time.