The low esteem is unwarranted. Economics, my own discipline, affords a good example. By assuming that all firms maximize profits as their sole goal and compete intently with one another only with respect to this variable, economists, using rigorous mathematical models, have examined how efficient and fair such markets really are. After patient and rigorous research over decades, economists know better and appreciate more what are the limits, including the moral boundaries, of profit maximization. Another criticism leveled at universities is that, because principles are taught tentatively and subject to revision, students are not given a firm foundation.
Universities engender, rather than resolve, doubt.
Young adults are unlikely to come to belief if their personal doubts, or the doubts expressed by society's leading cultural voices, are not freely and fully aired. At any university worth its salt, therefore, the pervasive role of doubt is routinely acknowledged. When Thomas the Apostle was incapable of believing in the risen Lord, his confreres did not throw him out of their community, but accepted him with good will, in the patient expectation that his doubt would be resolved, as indeed it was, in beneficial fashion for subsequent generations. In our age I hear it as carrying a prophetic and evangelical potential. I understand that bishops sometimes doubt whether Catholic universities are up to the enormous challenge history and divine providence have set them.