Not being on a varsity team may or may not affect your application (I am a sophomore and know many people who got in without playing any varsity sports in high school); however, you can combat this with outstanding CFA scores and other physical/sporty extracurriculars or accomplishments (like maybe consistently running in marathons) that you can add to your application. I believe that a lot of times USAFA looks at the importance of playing varsity sports for two reasons:
1) obviously, a high level of competition/athleticism, etc.
2) leadership opportunities available in playing on varsity (i.e. captain).
Because of this, if varsity/being a captain are not possible, look to accentuate your leadership qualities in other areas or clubs/organizations in your school or community.
If you do get into USAFA, a lot of intercollegiate sports hold tryouts at the beginning of the year for cadets to walk-on to their teams (just talk to other IC cadets or even the coaches about your interest). In addition, USAFA has a few different club teams that involve lots of running and are open to all cadets to tryout/join. Good luck!