It is how Safari does it but I'm not really sure what Apple was thinking. As far as I know, they very rarely use center-aligned text elements in UI that is customisable by the user. Left-aligned is better for usability, in my opinion, because once a bookmark is located in the bar, its position will not change unless the user manually moves it around. As it stands, the position of every bookmark changes to accomodate the addition of a new one; I don't think this is a good user experience.
As @TheJuli mentioned, having them centered also conveys the idea that they constitute an always important navigation element for every webpage, when the bookmarks bar should be best understood as a user-managed drawer whose items are always within reach.
Personally, I no longer use the bookmarks bar because of the center alignment, I have that much of a gripe. Instead, I just have regular bookmarks which I quickly access by typing into the address bar, or through the Start page.
