I don't disagree but then perhaps they should have worked harder to extend Wilkerson while lowering his cap hit for this year. If they got an extension done before Cox got his deal from Philly they may have even landed a bargain in comparison.
The Broncos are in a similar situation to the Jets with Von Miller and the franchise tag, potentially overpaying for their running back, and their QB situation, but they are coming off a dominant Super Bowl victory which soothes a lot of problems. Additionally, the Broncos appear, to me anyways, as having preserved a better relationship with the player they have under the franchise tag.
I am not necessarily saying the Jets did anything wrong because it is obviously a tricky process, but I also wouldn't say that they handled this situation optimally.