There's a lot of reasons why Apple doesn't want the Pre syncing with iTunes....
1. Apple doesn't support the Pre through it's call centers or technical support. You know there are Pre owners out there who call Apple for technical assistance with syncing with iTunes. This would be a huge headache for Apple's tech support and causes a lot of unneeded call volume.
How many pre owners are there? Hardly enough to clog up Apple's support team surely?
2. iTunes was deveoped to work with iPod as a companion. iTunes is essencially part of iPod, therefore they go hand in hand. Yes, Apple has a list of other devices that'll sync (and they probably pay royalties to do so), but Pre does not. Essencially, they're stealing abilities of other players that do play by the rules and pay Apple for Apple's hard work and infrustructure.
If this is so, why do Apple allow 3rd party apps to integrate wtih iTunes to sync? do the 3rd parties have to pay Apple for these features?
3. Apple pays a LOT to keep iTunes going. Bandwidth, servers, music labels, etc. Apple handles all of this, and the Pre only benefits from Apple taking all the costs of maintenance/infrastructure/music lablel royalies/etc.
Once again, Apple has no issue with people using 3rd party software to sync with iTunes (Nokia multimedia transfer for example). The same costs are incurred by Apple for those who sync in this way so it isn't a valid arguement.