Not necessarily a root cause problem, but it is still a problem that affects the quality of education and research.
Tenure was intended to allow for the things you're stating (i.e. academic freedom) without fear of backlash from donors. Unfortunately, as with all things there are downsides and one is having people who strive for tenure in order to ensure a stable job.
One thing that is a fundamental problem is how universities operate. There is inherent waste in everything that is typically done. Classes aren't designed so that the work you do amounts to anything beyond a grade for the class.
In a way, it relates to your point about perception. The perception of universities has changed because originally the university was for academics. College wasn't necessary to get a job. Now it's almost a necessity to find a decent job, but the way colleges operate aren't in a way that optimizes for that.
The problem with getting rid of tenure is that we have an up-or-out system in academia: you either rise to tenure, or you're fired. Permadoc positions would be nice, but if you eliminated tenure then academics would just become more abused, overworked corporate employees. Not because academic freedom would die, but because "if you don't publish X papers and bring in $Nx100 thousand research dollars this year, we'll get someone who will."
Tenure was intended to allow for the things you're stating (i.e. academic freedom) without fear of backlash from donors. Unfortunately, as with all things there are downsides and one is having people who strive for tenure in order to ensure a stable job.
One thing that is a fundamental problem is how universities operate. There is inherent waste in everything that is typically done. Classes aren't designed so that the work you do amounts to anything beyond a grade for the class.
In a way, it relates to your point about perception. The perception of universities has changed because originally the university was for academics. College wasn't necessary to get a job. Now it's almost a necessity to find a decent job, but the way colleges operate aren't in a way that optimizes for that.