Actually, they were originally started as legal institutions designed to give autonomy to masters and students from state and church interference in the training process. They were more like guilds than places to do scientific research.
The shift of focus toward science happened some time after the original universities were set up. Besides which, most of the important research done before Newton into what we would today think of as science happened outside of universities, which were (and for the most part still are, at least when it comes to science) _very_ conservative centers of thought.
But I agree with the idea that universities serve a better function when they focus less on commercial interests and professional training. When universities are commercially driven, they become conservative and narrow and, I think, do more harm than good.