Because the industry has changed. Years ago games were released as finished with the odd patch, then came the age of expansions, and now you've got games that're released - I wouldn't say unfinished, but by developers that continue to invest in their games. It makes sense from a business point of view to clamp down on mods.
Lets say, for the purpose of JWE that someone wanted five specific Dinosaurs (not yet included) and someone created a mod including those five and released it (for free). Frontier then come along with a DLC pack including those Dinosaurs, but wait, there's a £5 fee attached. The target audience/player-base has been split between those that want the official content, and those that download the mods 'cause it's free.