I agree that Perl is starting to gain a bad reputation on the web. mod_php is safe to use on shared hosting and mod_perl is not, which leads some people (even fairly experienced developers) to believe that PHP is just naturally faster. I've heard that mod_perl2 solves this with its perchild MPM, which (I think) gives each script its own namespace and runs it as its owner, but I don't expect speedy adoption.
Re^3: More than mod_cgi less than mod_perl.
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I think this version of mod_perl does address the shared hosting issue. The page I read (which I can't find right now) compared it to PHP's safe mode and also said it was a replacement for suexec. By changing the MPM, you can still offer all the power that the current mod_perl allows. I don't know anything about performance for either version.