It's not wrong at all for an atheist to not attend a parents funeral.
The funeral is really just for the people living to say their goodbyes and I'm sure if your mother was a good mother or your father was a good father then they would understand if you didn't attend their funeral.
My own son who is 13 said that he's an atheist and that because of his non belief in god that he could not attend my or my fathers funeral when we go.
I completely understand and I'm not religious myself and if my son does not want to be at my funeral it's okay with me.
I'm not gonna be aware of the funeral anyway because I'll be dead and not conscious.
If you don't want to attend your parents or someone's funeral because of your beliefs then it's okay.