I was thinking that it would be nice to have a way for there to be a setting that you can set so that only certain members of a server can go through each portal, even if all the members are op's (aka a group of friends playing on a private server with out any permissions, except for the ones that are in the plugins that the server owner uses).

OPs automatically get all permissions. I wouldn't want to deny anything to an OP.

I doubt this will happen (let me meditate on it a bit) but this kind of per-portal permission is not really intended as the use of NetherPortals. You should try Multiverse-Portals if you want the fine grained control.