The problem, in my opinion, is how external entities treat science. Some examples:
* Media reporting low grade papers as "Science" which constantly contradict each other. "Scientists found out $something causes cancer", then a year after that "Scientists found out $thatsamething cures cancer
* Pseudo scientific drugs being sold for a health-and-beauty-obsessed general public with little to no effect
* Political think tanks funding flawed research to push their own agenda and heavily echoing those researches in their echelons for political gain
It seems that academia has become a foundation for other entities to cling on for profit, and now the it's the acamedia's reputation that has been shattered.