Frankly, in my opinion, most of the talk about the "bad parts" of Austin (specifically the areas that UT shuttles service) is due to racism. Austin is still a highly segregated city, cross I-35 and you enter into the historically black part of town. That combined with the depressed economic situation in that area of town causes a lot of people to decry it as a "bad area." I know many people that live in this area as students, and none have had any problems, while people living in the more rich/white/student-y places have had a lot of trouble with theft.
I think you'll be just fine finding a place along one of those shuttles, and your rent will be cheaper too.