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I tend to use a Makefile* for running coverage reports. Here's a relevant snippet:
Customized a bit for a Mac, but the relevant parts are the PERL5OPTS ENV I'm setting, which points out how to ignore things using -ignore and +ignore - as long as you know the syntax it's expecting, the docs should clear things up. In a nutshell, I'm telling Devel::Cover to ignore my .t files, as well as the prove utility. Fascinating yes, but like you, that's not what I really care about :)
You don't necessarily need a Makefile for this, simply typing the following into an appropriate command line** will work***, too:
Update: changed the PERL5OPT line a bit, added a little more explanation.
* I'm not great with Makefiles, but the above works for me.
** i.e. some unixish shell, other OSes may not let you specify environment variables like that.
*** assuming your test files are in `cwd` and named *.t.
In reply to Re: Setting Devel::Cover options for a web application