Java is a nice introductory language, it is pretty ubiquitous, and it is platform agnostic. Those are likely the primary reasons for schools using it so frequently in computer science departments, the University of Colorado does anyway (and interviews I've conducted lead me to believe that is normal).

When Cisco reported that 91% of attacks exploited Java vulnerabilities, it triggered some concerns.

Just take a minute and think about how shocking this is.
Android is largely written in Java. No surprise that Android sees 97% of malware in the mobile space.
Schools are too slow to adapt to changes in the real world.