Since you are running under mod_perl you need to tell Devel::Cover to look at the code that's being run by apache. Put something like this into your startup.pl. (Or modperl_extra.pl if you are using Apache::Test which I recommend anyway for testing a mod_perl application).
use Devel::Cover ('+select' => 'My/Module', '+silent');
Then I would recommend that you look at using something like Module::Build
to create your test harness. With it, you can simply run make testcover
and it will take care of making sure the test harness has Devel::Cover enabled.