I must admit that the first time I looked at Dropbox, the single folder design made me stop the train. It wasn't until months later that I realized I could set up symlinks. It was a bit of an "I feel like a dumbass" moment.
With this in mind, it's easy to see that the Dropbox made the right design decision. With symlinks, the problem was already solved for them in a way that power users are already familiar with.
So the problem Drew mentioned, of mapping between different sets of sync folders on different machines, is transformed into mapping an identical folder hierarchy (i.e. the dropbox folder and contents) to arbitrary sync files/folders, done by the user, for that specific machine.
You get the simple, instant user model (dropbox folder), which you can customize to any arbitrary user model, as much or as little as you want, when you want it. And simple syncing.
If you're a Windows user think of a more hardcode version of shortcuts. You can create them in Windows Vista / 7 from the command line through the `mklink` command.
Basically you can set up a symbolic link from inside your Dropbox folder to any other directory and Dropbox will start syncing the folder without you having to actually copy or move files.
With this in mind, it's easy to see that the Dropbox made the right design decision. With symlinks, the problem was already solved for them in a way that power users are already familiar with.