Before damning this idea, let's look at the other side. STEM majors will make much more money during their career than a liberal arts major likely will. That way, spending a little more on an education is a better return on investment. This also allows students (hopefully) to see a direct return on their investment in the quality of their education. If you are expected to pay more for your major, hopefully, this will be reflected in the facilities and instructors offered. On the flip side, it could also bring in more people who were turned off by high prices for majors that will not result in high paying jobs. I'm currently working on funding for a masters in architecture, a job that pays less than, say, engineering, and costs just as much tuition wise. Allowing variable rates lets them maximize their profit while allowing students the opportunity to pursue whatever major they choose.
This is, however, highly dependent on the rates chosen and how the money is ultimately spent. As always, if your product costs more than it's worth, then you'll end up losing buyers.