Lots of reasons not to use perl :-)

Speed. Sometimes you need to do something faster than perl can.

Space. Perl's data structures are optimised for speed rather than memory usage. Sometimes that can cause problems if you're dealing with lots of data.

Appropropriate functionality. If I have to write a multi-platform GUI I'd probably pick Java/Swing over any of the current perl solutions. If I have to do a lot of predicate logic stuff I'd pick Prolog over current perl solutions. Etc.

I use perl most of the time - but only because perl is the best solution for most of the stuff that I write ;-)

There are also non-technical reasons.

For example, if you have a project that is mostly in language X, then it's probably easier to keep everything in X rather than switch part of it over to perl, even if its more suitable technically.

I switched part of a web project over to perl when most of the rest was C++ (because DBI & LWP made things almost trivial).

Bad decision on my part.

The extra overhead of another language (the glue between perl/C++, different style of test suite, having some of the team not understand what it did, etc.) caused far more problems that making part of the project easier to implement.