The obvious answer is to cry foul play and demand it be included, all or nothing.
The non-obvious problem is that perhaps they really can't get enough support for the bill in the mid-west and southern states to get it passed.
I personally feel that it would be better to get the hate crimes bill passed, and then to return to the issue for transgender inclusion in the bill later. Having a good law that protects most of us, and most of the transgender implicitly, is probably better than not having the law at all.
But I feel like a traitor saying that.