Winfred Tubbs was an outstanding linebacker in New Orleans because the Saints allowed him to roam on the outside and use his natural athletic ability to make plays. When he came to the 49ers, he played inside and was not the impact player the 49ers had expected. The other problem with free agency is that players often have played their best football before they became free agents. What a team sees in a player before he becomes a free agent is not necessarily what it gets from that player. None of those problems occur with drafted players.
Teams can put rookies into their system and determine very quickly if they fit.
And the rookies have young bodies. Even if they've been injured in college, as many have, they're young enough to recover and still help a team. Most of all, when teams draft players, they usually come with a low price tag, especially if they're drafted after the first round. If the players are good, the team will have them for four years at below the market price for their ability. The 49ers have been forced to go young.