The first and easiest possibility is that you don't have the axle seated firmly in the dropout on one side of the fork, and therefore the wheel is sitting cockeyed and out of position relative to the brakes. Check that first, but since you say the brakes are hitting the tire, it sounds like you may have knocked the brakes out of whack when you removed/installed the wheel. Good instructions here for linear pull brake adjustment:
http://www.parktool.com/repair/readhowto.asp?id=21