Sure. I think abortion is sometimes morally acceptable, other times not. During the first trimester of pregnancy I think it is virtually always acceptable. In the second trimester I think it is only acceptable if there is a health risk, a major deformation in the fetus, or in the case of conception by rape - I would argue that a woman should get an abortion as soon as she knows she is pregnant if she does not want to carry the child. In the third trimester I think abortion is usually wrong (unless there is an extenuating and major health risk to the mother), since the child could likely exist outside the mother's womb at that point. A c-section would be a better option.
I do believe that no woman would really want to harm her child, so I have little issue with deferring to the judgement of a mother to decide when she should like to bring a life into the world.
Also do keep in mind that I do not speak for all atheists at all, everyone has their own views on this issue and our views are of course influenced by our culture and society.