My first "real" MP3 player was a 2nd Gen Microsoft Zune. I also have a Zune HD. Both of these devices have WiFi sync that works without a hitch so I was thrilled to hear that iOS 5 would include WiFi sync. When I first set it up it worked beautifully. Since then, however, it has been hit-and-miss with mostly a miss.
Fail number one: If you leave that checkbox enabled next to "Open iTunes when this iPhone is connected" you will A) drain your battery faster when you're on WiFi with the iTunes host and B) won't be able to make iTunes go away for more than a couple of minutes on the host. What happens is that as long as you're on the same network, these two keep a connection to each other as if you had the cable plugged in but weren't syncing. It causes the phone to constantly tell the host it's plugged in, thus actively using WiFi and draining the battery, and causes iTunes to re-open every couple of minutes because the phone has been "plugged in." The Zune software can distinguish between a wireless and wired connection and only auto-launches on a wired connection. On the Zune, if you want to keep the system available for WiFi sync it's easy enough to do because the Zune software isn't such a RESOURCE HOG as iTunes.
Fail number two: If I go into Settings > General > iTunes Wi-Fi Sync, most of the time the phone doesn't see the host as "online" and can't complete a sync. This occurs even if the aforementioned checkbox is left enabled.
What's the point? Why would I want to leave a feature enabled that rapidly drains my battery, annoys me on the host system and doesn't work most of the time? Apple, I would give you an F for Fail but you did make a good effort to enable the feature so I give you a D for Doesn't Work.
Note: I did not include the iPad in this rant because I sync my iPad with my laptop, which is off most of the time, and do not know if the functionality is similar.