I use the VPN all the time to log in to one of my clients networks using CISCO certification, then once connected, use one of the (many available) Apps, PocketCloud for remote desktop connection.
admittedly I had to hack the PCF file, (as the IT don't support iPhones)
Works fine over WiFi or 3G.
Presumably it is built the same as native VPN on Mac
(Think of it as a tunnelled line to the sever where you are trying to connect, and then you run over that what ever App/ protocol you want to use)