Well, there are some reasons not to use mod_perl. The main reason is that there is only one Perl interpreter instance (actually, there is one per worker process, cloned around forking the worker process). It runs inside the Apache process. Forking and cloning may cause some minor trouble, but that's rarely a problem. Mostly, this affects DBI, and Apache::DBI knows enough of DBIs internals to handle most of the problem. On Windows, Apache does not fork (as far as I know), but creates threads instead. So, everything runs in a single process.
The real problems are:
all applications have to share the one interpreter (per process)
all applications run in the process context of the Apache process
a single application error kills the entire Apache process
a single application error happening before Apache forks its worker processes kills the entire webserver
So, applications are de facto not isolated from each another, and you can not use operating system permissions to limit access to only one application or to the web server.
Compare with FastCGI:
The FastCGI process uses a single Perl interpreter for each application.
Each application runs inside its own process context, so you can isolate the applications using different users, filesystem permissions, chroot jails, and so on.
FastCGI communication uses sockets, either local ("Unix") sockets or TCP sockets. So you can run applications on different machines, perhaps behind firewalls that further isolate the web server.
FastCGI is available not only for Apache, but also for Nginx, IIS, Roxen, Lighttpd, and several other servers. So you don't have to re-invent the wheel just because you switch to a different webserver.
Of course, because FastCGI runs outside the Apache server, you have some communication overhead. And you can't use all of the Apache internals that mod_perl offers but rarely anyone uses.
Today I will gladly share my knowledge and experience, for there are no sweeter words than "I told you so". ;-)
Thank you for your thoughts on this. I had a discussion with a friend of mine and I had the same issues you just brought up about the Perl interpreter instance. I did not know about the other issues, so again thank you for enlightening me...