Yes! Your religious background, or lack thereof, is immaterial. Your wedding is about the commitment between two people, not the beliefs of any organization.
It should be noted that some religions may not recognize a marriage that takes place outside of the church. If this bothers you, I would suggest that you talk to a minister/priest/etc about what it means to be married in that particular religious organization.
Rest assured, your marriage will be recognized by the government, provided the proper documents are signed and fees paid.