My wife is laying here in bed crying her eyes out because she's scared I'm going to leave her but I'm not. She does want to be alone right now but I don't want her crying alone but I hate to see her cry. How can I comfort her ? What should I say to her ? I'm also a girl.

Make sure she has enough tissues.

Did something happen today to make her feel this way, or is this a fear she's always had, and it's just worse today than it normally is?

I know that when I'm crying, I'm upset, I tell my husband that I want to be left alone, but deep down I really want him to come to me, hold me, comfort me, tell me it's going to be okay. We girls often say one thing but mean another, don't we?

I would go into the room and tell her that you really want to hug her, comfort her, just sit with her, but if she really wants to be left alone, you understand. Let her be the one to tell you what she really wants. Just try to be supportive.

Once she calms down, I would have a very serious discussion about why she feels that you're going to leave her.

There has to be a reason for her to think you may leave her. Try to reflect and see if you can remember anything that may have happened to make her think that. OR , just for arguments sake, is she acting out looking for attention? It could happen.
I am glad to see that same sex marriages have the same problems traditional marriages do!@

When she is crying, normally do or say nothing, just be there.

Latter you need to discuss why she feels this way, normally there is something happening, or not happening to make her feel this way

Kind of wondering how this all turned out.

How old are the 2 of you and how long have you been together?