I think it's a bit misleading to say that it's "all the same tree". In fact, it's two separate databases, one online, one on your local hard drive, which FTM can be configured to automatically synchronize. But with FTM you have the advantage of still having access to the local database even when Ancestry.com is unavailable.
I don't automatically sync in FTM, for a number of reasons, one of which is that I don't want work in progress being dumped online. I also prefer having local backup copies of my databases (e.g., in GEDCOM format) for data portability, or in case I should decide not to renew my Ancestry subscription just because I don't want my work locked into Ancestry.com.