No. Once you purchase FanDraft, you can use it as many times as you would like, for as many years as you would like. Even if you decide you don't want to purchase future upgrades, you can manually enter in future NFL rookies, and re-rank players to your liking.
FanDraft has come out with annual upgrade every year, which includes new features and an updated NFL Player Database. Registered users can purchase the update for 50% off the regular price.
Note: Top Overall rankings for the "Top Overall" feature cannot be manually changed without upgrade, and you cannot integration with present year MyFantasyLeague leagues without having the most recent version.