NYRR is attempting to find a solution to a complex problem, and all anyone can do is complain. Setting aside everyone who despises the whole idea of transgender identity, prevailing wisdom here is that it's not fair to women. I feel like it's a good compromise and a starting point, not necessarily and ideal solution. It seems like NYRR has decided that $5000 is a small price to both recognize transgender runners and divert them from competing in the women's division.
You can argue about all sides of the transgender issue, but I think this ultimately helps and removes controversy from the women's division by providing a separate category for transgender runners.