As long as 'protection' does not end up meaning being a favoured or special priority......I think that is the crux of the issue.
If it was only women that had toilet provisions that were meant to specifically cater to their needs, and men didn't - then that would be negative discrimination with women being seen as being given special privileges and priorities.
Or if women had first priority on using a set of toilets, and men had to wait until all of the women had used them first before they could use them, that would also be a case of negative discrimination.