When you say "multiple urls" do they each have their own Moodledata and Databases, i.e. one Moodle code base but separate sites?
If not, that is if you have ONE moodle
database on different domains I think you are storing up trouble for yourself.
The reason your wwwroot is not working maybe because you are calling via the command line as opposed to calling via the
URL?
If so there is a way to get it to set the
domain on the command line but I cannot remember how that was done (sorry).
Another way to call cron is using wget to pull down the URL which would work if you had an entry for each separate domain, for example
wget http://domainone/admin/cron/php
You would want to stagger them to call at different times.
The other thing with wget is by default it will store /
download copies of the cron.php output from Moodle which you may not want.