It's obvious that the reason perl lost so much market share for PHP are the difficulties with mod_perl. I would blame here a variation of the TIMTONWTDI
Of course we are only talking about one specific market here - web applications. PHP is certainly not making in-roads in the use of Perl for system administration, testing, build management, telecommunications, etc.
I don't think that the number of different ways of setting up mod_perl is the issue. The reason PHP is used more is that it's basically impossible to setup mod_perl for a shared hosting environment in a secure way. PHP does it out of the box.
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