In addition to the reduced damage somewhat taking the place of the MR, Kassadin doesn't fight with enemies in the same way that other melee champs do. Most melee champions, especially tankier ones, like Kassie, have to wade through a barrage of poke and harass to get their enemies, so they need the MR to survive with a decent amount of health. Kassadin's Riftwalk allows him to close gaps so efficiently that he doesn't need the extra MR as much as, say, Garen.
Other melee assassins, like Katarina and Talon, do gain MR per level, but Kassie isn't really like them, either. Their job is to get in, blow up a carry, and maybe get out. They need the MR to keep themselves from vaporizing before they can pull off a combo. Kassadin, though also an assassin, tends towards a much more skirmish-y style then either of these two examples, so the MR can also be somewhat replaced by the inherent tankiness of his build.