Why is Nanavira considered controversial?
If I had to speculate I would suggest that he was very intellectual.
That can be intimidating.

From the site Nanavira.org:


  Notes on Dhamma has been variously described as "arrogant, scathing, and condescending", as "a fantastic system", and as "the most important book to be written in this century". The Ven. Ñānavīra Thera himself remarked of the book that "it is vain to hope that it is going to win general approval... but I do allow myself to hope that a few individuals... will have private transformations of their way of thinking as a result of reading them".