The Rule 5 Draft exists for only one reason, and that is so teams cannot hoard talented players at the minor league level that other teams would be willing to use. Teams pay $50,000 to select a player and must keep that player on the active roster for 90 days or be offered back to the original team at half the price. Last year, the Cubs lost relief pitcher Andrew McKirahan to the Marlins (he was subsequently traded to the Braves).
Here’s a little bit more of an explanation on Rule 5 eligibility, courtesy of Baseball America:
Major league teams must protect players on their 40-man rosters within three or four years of their original signing.