I think you're both on-track, that the document hasn't finished building (and therefore the element probably doesn't exist) when I'm trying to set the focus. However, I solved the problem the easy way: editing the source code.
I just added
this.tagInput.attr('autofocus', 'autofocus');
to the _create() method of tag-it, which gives the focus to the element without having to resort to Javascripty goodness. This worked.