I could be wrong, but I think I know where some of the confusion comes from.

Bookmarks, despite the fact that they're the primary means through which a normal user would access their server(s), are downplayed in the UI. They don't appear in the "New Connection" window that appears on launch, which includes the recent connections (double arrow) pull down and would be easily misinterpreted as being related to bookmarks. Then there's the toolbar in the app, which includes a prominent Favorites folder, but there isn't a Bookmarks folder or icon. The only way to see bookmarks is through the top menu.

This confused me to no end when I first starting using Yummy, but I eventually got over it. That's not to say it's a good solution for bookmarking. At the very least, Bookmarks need to be incorporated into the New Connection window (how many people consistently enter new server data anyhow?), with the recent connections relegated to the Application menu (a la "Recent Documents" in other desktop apps).

My 2 cents.

How about bookmark syncing with .Mac? Transmit does it, and it keeps all three of my Mac's in sync with my FTP connections.

Ah, very interesting! Thanks for the tip.