Synching using iTunes is supposed to be a two-way job but as I don't own an iPad I can't verify how it would work with Safari bookmarks ...
How about either attaching the file to an email and sending it to yourself or use something like a Dropbox (free) account.
You can add files to your DB folder right on the iPad and they drop right into your DB folder on your computer. It's pretty quick too. Only "problem" is your computer needs to be on the net. But it's great because DropBox actually backs up whatever you put in there for 30 days or something to that effect. So if you delete something, you can restore it for a period of time.
Here's my DropBox referral link:
http://db.tt/CmtEABgF
From that link you'll get the download for your Mac and from this link you'll get the iPad app version.
http://www.dropbox.com/ipad
For every friend who joins and installs Dropbox, we both are rewarded with 250 MB of bonus space (up to a limit of 8 GB) so it's fairly handy. I discovered Dropbox from researching an answer to your issue and joined up as it sounded good and my MegaUpload account is now bottoms up
Hope this helps.