There are some alternatives, Rich.

First, if you have a MobileMe account, you can use that until Apple shuts it down on June 30.  Many BookMacster and Bookdog users have been doing that for years.  On the surface, it works the same as iCloud.  Just substitute "MobileMe" in our documentation wherever you see "iCloud".

Understand that all this is regarding Safari bookmarks on your iPad.  Apple has effectively walled off ("sandboxed") Safari bookmarks on iOS devices.  There is no way to get Safari bookmarks in or out on an  iOS device without jail-breaking it.  The only hole is via MobileMe or iCloud and a Mac app.  Since that has become tricky with iCloud but not impossible, as far as I know, BookMacster is the only Mac app available for doing that.  (I've not much time to spend researching other tools – anyone who has found another app or method which can reliably export to Safari and iCloud is encouraged to reply – if true, I'll stop making that claim.)

Your other alternative is to find an iPad app which can sync your bookmarks via Dropbox or some other non-Apple server, but your bookmarks will be in a separate app.  You can visit one of your synced bookmarks by launching the separate app, selecting the bookmark and then clicking Visit in Safari, or something like that.  There is probably no way to create a bookmark in the separate app while browsing in iOS Safari.  So it's limited.  I read some time ago that Xmarks has such an iPhone app and I assume there's an iPad version now.  Again, anyone who knows better can correct me.  Actually, I'd appreciate the research, since I'd like us to make a similar app one of these days and we'll need to know what's out there 

Beyond that, call up your contacts inside Apple and tell them you'd like some attention paid to Problem ID #10473679 in their Bug Reporter (internally, they call it radar.)  The title of Bug 10473679 is Third-party apps cannot access Safari bookmarks, and it was submitted by me on 2011 Nov 18.  Or submit here:

www.apple.com/feedback/macosx.html

or to make it more formal, with your Apple ID,

http://bugreport.apple.com

I suspect that the chances of Apple even wanting to fix this are pretty slim.  Saying that you're switching from Safari to some other, more open web browser is probably going to be the most effective approach.