Were you syncing your bookmarks with the computer before?
If so when you set up MobileMe iTunes probably changed those sync settings.
You have two options. Setup your computer's browser to sync with MobileMe, then turn the iPad's bookmark syncing back on, or re-enable direct syncing with the browser through iTunes.
I'm not sure how to do the first on anything but a Mac, but it would probably be done using the MobileMe utility that you (may have) downloaded. {On a Mac it's in System Preferences, MobileMe, the Sync tab}
For the second, connect your iPad to the computer and select it in iTunes. Go to the Info tab and make sure you've got bookmark syncing turned on and pointed at the right browser. Since you have a MobileMe account setup it may warn you that syncing is happening through MobileMe. As long as you have the bookmark syncing turned off in the Account settings on the iPad, you should be fine. Don't turn them both on.