the main thing i like better about php is that its an embedded scripting language. the php files can contain both the html and the php intermixed however you want to code it.
with perl you can accomplish the same thing with server side includes, but its still a matter of connecting all the html pages to the scripts in the cgi-bin. passing variables or making variables global to all files can be overly complicated in perl, if you are working on a web app with multiple files.
personally i find it much more efficient to have it all in one place. mostly an organizational preference, i guess. if its just a one shot script perl is great, but if you are building web apps i think php is just geared more specifically for that kind of thing. it has session management and database functions built in. you can basically do the same things but with less code.