Disregard my previous post. The following post is clear and correct:
The Mac App Store is for MacOS X applications, the App Store is for iPad, iPhone and iPod Touch apps and the iTunes Store is for Music, Movies, TV Shows, Podcasts.
I was incorrect in stating above that iPad, iPhone and iPod Touch apps are iTunes products. They are NOT. They are App Store products. If your company must go the route of individual iTunes accounts for every user, that is certainly one way to do it.
If, however, you are inside the US, having one corporate iTunes account and enrolling in the VPP program does allow you to legally use that one account to run the same application on 5, 10, 100 or 1000+ iPads. You will, however, have to pay for the app 5 times to install it on 5 iPads using that single VPP corporate iTunes account. You will have to pay 1000 times for the app to put it on 1000 iPads.
You tell the VPP program the apps you want to buy and how many of each you want. They then send you an email with a spreadsheet of activation codes. When an activation code it used on one iPad, it may only be re-used if it is uninstalled from that iPad first. The VPP program is there to make it easier to manage all the apps on corporate devices and centralize payment to a single authority which can then send the activation code or codes who whoever needs them.