It was widely believed that during the 2004 draft, the Tampa Bay Buccaneers were really interested in Vilma. Rod Marinelli was an assistant coach on that staff and Joe Barry was serving as the linebackers coach at the time. The Jets, however, drafted Vilma at 12th and the Buc's settled for Michael Clayton. So both Rod and Joe knew about Vilma and liked him when he was first coming out of college.
Numerous reports say that the Jets were seeking a 2008 3rd round pick for Vilma and the Saints reportedly ended up trading a conditional 4th round pick in 2009 that can be upgraded to a 3rd round pick. So why didn't the Lions take a shot on Jonathan Vilma?
Well, the salary cap may have had something to do with it. Jonathan Vilma has only one year remaining on his contract and will be a free agent after this season. If the Lions were to trade for Vilma, they would want to lock him up to a long-term contract extension. If they would have taken a chance on Vilma. They would have traded a conditional 4th rounder to the Jets and locked him up to a long-term contract, likely having to give him in excess of 10M in guaranteed money. If the knee doesn't hold up, they would be out the conditional 4th rounder in 2009, $10M in cash and salary cap space. The $10M in cash and cap space would hurt the Lions a lot more than the conditional 2009 pick.
Some would say, well then don't sign him to a long-term deal, just trade him and keep him for the last year of his contract and then make the decision. Well, if they were to do that and say the knee does hold up. The conditional pick would probably be upgraded to a third rounder and Jonathan Vilma would be a free agent after this season with no obligation to sign with the Lions. He could agree to sign, but there would be no guarantee that we could keep him long-term.
It's fairly obvious that even though the Lions say that Vilma passed the physical, they weren't 100% sold on the stability of the knee.