Reunion is a far more solid app and is well supported. It won't let you down. The user interface is well laid out and easy to pick up. It is not phased by same sex marriages, adoption, or any of the other non linear family bonds. I thoroughly recommend it.
I have recently bought Family Tree Maker 2011 for Mac because of the integration with the site but so far I am not impressed. I assumed that it would be fully synced to my web-hosted trees. Instead I find that you download the whole tree. While it is true that you can then run the web-based searches directly from the computer-based tree you would then have to do the whole thing again to update the web-based tree. What good is that to anybody? Although you can upload the tree back onto the site it has to be a new tree so you start from square one and you would have to re-invite all your collaborators. This makes the whole integration thing ineffective.
So, as things stand at the moment you can integrate with the site equally well with either app. My advice is to pay the extra money and go with Reunion. It's just better.
There is only one smart reason for buying FTM as well: if you buy it as part of a six month package you can think of it as getting the app thrown in for free. This is what I did, so I don't feel bad about having bought the app. I will continue to use Reunion with the Ancestry website as my principle research tool because it is the best resource out there and if they add syncing to future versions of FTM I will move over because that would make it invaluable.
Hope that makes sense. Good luck in your decision.