My point is that Perl isn't giving itself a chance of competing for mindshare in web development college courses because of the compatibility and usability headaches.

Which usability issues are you talking about? As shown in the other other responses, there are plenty of "out of the box" installations of mod_perl (even on windows). Also keep in mind that mod_perl has a different goal than PHP: it is supposed to give direct access to the Apache API, and thus is a lot tighter coupled to specific apache versions.

If you don't use things like Mason or Apache::Template how do you separate your presentation and business logic? How do you implement templating? Seriously, I'm interested in alternatives.

Mason is hardly an example of a clean separation of business logic and presentation, and neither is Apache::Template. Modules like CGI::Application or Apache::MVC do a much better job of it, IMO.

Joost.