I have the following in my .vimrc:
\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"\"
An idea in need of implementation:
You could write a function which, when called, checks if the only buffer remaining (or perhaps the only non-help buffer, if you prefer) is a NERDTree buffer and, if so, deletes it (or just quits).
Then have an autocmd run it whenever a buffer is deleted / hidden / whatever actually happens when you :q (it shames me to admit I'm not entirely sure!).