The beginning? No. It's more the early-mid game, where you're asked to venture outside of the southern cities, that things start to get interesting, because you start running into tough enemies but probably will not be well-equipped to deal with them by that point.
For me the appeal of Morrowind's magic system is probably the sense of mastery you get over the world and your abilities. You start out being some nobody schmuck, only to end up flying everywhere, being totally unconcerned with the affairs of regular people, walking through hostile enemies without them even noticing you're there, brewing potions and creating spells that let you do totally crazy shit, destroying lesser creatures with a wave of your hand, etc. It's basically the ultimate magical empowerment fantasy, without being focused on combat, and as a result it's very rewarding.