I will attest to the fact that even with shorter commutes, like the OP's, pants can get destroyed in no time. My partner only rides about 20 miles per week, and she recently noticed that a pair of corduroy pants that she'd had for years had worn really thin on the, ahem, seat part in about two years of commuting - and she doesn't even wear that pair all that often when bike-commuting. I myself have thrown out more than my share of pants due to the wear in that region.

A seat cover or a smoother seat might help. It won't eliminate the friction entirely, but may reduce it enough to be worth a shot. 3.5 miles is a short commute, and it's a bit of a hassle to have to change before and after every single day. It's not as though this kind of a distance will have you arriving at work all sweaty and smelly, necessitating a shower and a change of clothes, especially if you aren't riding up a mountain or trying to beat any speed records.