I havn't checked if this is true, but a wild guess would be itunes showing the downlaoded app sizes, while the ipad, the apps+app data. (like spotify, small app + 1.4gb music)
A lot of apps take up more space than the download size quieted in the app store. At a guess I'd assume they decompress the graphics (or something like that) when they install.
If you go to Settings/General/Usage/Manage Storage you can see the usage broken down by each app to see the worst offenders.
If you have any files that were downloaded straight to the app like video files in AVPlayerHD then they show up as space taken up by that particular app.
For example my iPad says that AVPlayer is taking up 10gb on my iPad, which the app itself is clearly not that big. If you go to settings>general>usage, it'll show you which app is taking up what space.
EDIT: Just noticed Ries said the same thing above.