No stupid questions.. Facebook is extremely confusing, and there's a lot of variables in play. We try to 'tame the beast', and as an admin, you should try to know what's going on under the hood
When a user registers on your site through Facebook, they need to approve your application. By doing this, they're giving permission that your application/site can see their Facebook User ID, name, and a few other 'basic' profile fields. The extra permissions are for things above and beyond this. If you don't set those as required, then you may not be able to access that information.. so without email permission, you'll get a 'proxy' email from Facebook which hides the user's real email, and all emails from you will be scanned by Facebook to make sure they aren't spam or that you haven't sold it to a 3rd party.
By setting them to not required, if JFBConnect needs those permissions (you want to post to the user's wall, but don't have that permission required), we'll request that permission of the user when we want to post. If they decline, they can still continue to log in and won't have a wall post.
So, if the permissions are set to required, the user simply won't be able to login to your site (through Facebook) without giving you those permissions. If they're optional, we'll try to get them to grant the permission if we need that information (to fill out a profile, post to wall, etc), but if they do not want to provide it, they'll still be able to login.
Long answer.. hope it helps!