If you click on Store, in the menu bar of iTunes, then on Authorize This Computer.... that will allow any apps (that have been purchased or downloaded on your iPad, with the same account as the one used to sign in to iTunes on the computer) to be transferred across from one to the other (You can also just click on, Check for available downloads. in the same menu.)
Less likely, but it can happen if you use more than one account. If some were downloaded while signed into a different account from the one used in iTunes on your computer, or from one you no longer or don't normally use, then these can't be copied over as Apple cant verify that you are the rightful owner of the software (even free ones) unless the same AppStore account is used on all of your devices and iTunes.
For example I use a different account for iCloud than i do for my AppStore and iTunes purchases. So I always have to make sure that the one I use for purchases is the one all of the stores are signed into. If I setup a new device and forget to click on the button to setup both accounts during the initial device setup process. Then by default I get signed into the AppStore using my iCloud account and I don't notice until I go to transfer apps to iTunes and it doesn't work.
(I've also, for some goodness knows what reason, been signed into the AppStore using my iCloud account when I have put in both sets of account details. So it's always worth checking in settings if you're signed into the right account before making purchases.)