Generally speaking, a minority of Bach scholars question the piece's attribution. Christoph Wolf, who is for many the top Bach authority does not question the piece's attribution at all.
For what it's worth, the mark's against Bach's authorship can mostly be explained away. There is no direct evidence against his authorship, unlike some other works where the authorship is more easily disputed.
Just to take two:
- Parallel octaves throughout the opening of the toccata
Writing Parallel octaves, while strictly forbidden in counterpoint is a very natural thing to do on an organ, especially if youre options for registration are limited. Essentially, to make the organ play louder a composer would have to write harmonies with more notes. Bach wrote many pieces to demonstrate how loud, and powerful the organs he was using were.
- True subdominant answers in the fugue
This is perfectly normal in Bach's work, and was known before Bach's time. Buxtehude did this.
There are many theories for why the piece is so different (it was written for Violin, or by a younger, more improvisatory Bach)
Compared to other pieces accused of being misattributed, for instance the Albinoni Adagio in G minor (which is certainly forged), there is little direct evidence to prove or disprove Bach's authorship. Just criticism of style.
This forum thread has some interesting discussion on the topic: http://classicalmusicmayhem.freeforums.org/bach-attrib-toccata-fugue-in-d-minor-bwv-565-t1818-30.html
As of today, no one has definitively proven it wasn't Bach.