She messaged me after 3 months of no contact? It's bothering?

I hope you guys and girls would be patient to read this and could help me figure out my situation.

Last 2 days, she messaged me out of the blue saying sorry what happened before between us. Here is our conversation:

Her: Hi. I just want to say sorry from everything. I should've said sorry earlier. I am really sorry. Mostly from what happened before. I am sorry.
Me: Hi. It's okay. I am already okay with it.
Her: Sorry and thank you!
Me: Okay, that is nothing.

*Conversation ended*

I never expect that she would message me again since she had been straight forward and rejected me.
We have dated for 3 months. She know she means a lot to me so it hurts like hell when she asked me to stop pursuing her. I thought everything was alright...

Now, it really bothers me. Like what the? It's been 3months already and I have decided to move on, now she comes back saying sorry.

What I thought is she feels bad about it and just to have a relief on herself. She doesn't really care on the damaged she cause, she cares only on herself.

Honestly, I still have feelings for her and attempting to ask her if there is still a chance but I suppressed it knowing that she had already rejected me and as far as I can feel, I am no one to her.

Answers will be appreciated very much. Thank you.
She messaged me after 3 months of no contact? It's bothering?
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