I found NERTree really akward and was one of the reasons why I originally had trouble switching to VIM from textmate.
Its best to use something like PeepOpen, command-t, fuzzyfinder to open files. If you want tree structure I just use terminal and aliased:
alias l='ls -AlGFh'
Or use the vim directory navigation.VIM also looks much nicer with just a single file open. The left panel for NERDTree looks hacky.