Because they're men.
Why do we keep any men out of women's toilets and changing rooms?
IMO it's mostly safety and comfort. Men are more dangerous than women and are generally larger, faster, and stronger, with longer limbs, stronger grip, etc. Men are more likely to commit violent crimes including rape, sexual assault, murder, etc. They are also more likely to commit sexual offenses than women.
Those things are still true after men transition. Offending rates are similar before and after transition. They are still stronger, faster, larger, etc. Why should we treat them differently just bc they feel like they are women?
Comfort can be for many reasons. Many ppl have cultural or religious beliefs that say that women should not be in private spaces with men they don't know. Even without those beliefs, many women are uncomfortable being in a vulnerable position with men they don't know well. (See safety, above.) Most women don't want to worry about voyeurs, hidden cameras placed by men, exhibitionists, etc.
Many women have experienced male violence and are therefore afraid to be around men, esp when they're in a vulnerable position, like a toilet or shower. Some, like me, have some kind of PTSD and get triggered by men, esp in areas like loos or changing rooms. Triggering means that I relive my abuse for hours or days. Why should I have to risk that just to use the toilet? Even if I want to view trans women as women, my brain will react as if they're men.
For me, the bottom like is "Men are afraid women will laugh at them. Women are afraid men will kill them." That's not hyperbole, and many men don't seem to understand that at all. Why should women have to deal with that if they want to use a public toilet?