When you catch the ball close to the line there are a lot more guys to tackle you.
A guy like Tyreek Hill has really good YAC because he often runs by one DB and gains 40 yards of YAC off it.
Golden Tate caught the ball closer to the LOS and got more yards per catch. Albert Wilson nearly doubled Landry's RAC production. Tyreke Hill has a really good YAC because he's capable of consistently catching passes down the field.
You are simply much more likely to get better yardage throwing the ball down the field. In that link, it says that the expected yardage from throwing the ball to the worst catch % in the league (Josh Doctson, 44.6%) is higher than throwing it to Landry. Sure 45% completions look terrible, but it moves the ball more than completing 66% to Landry, thus puts more points on the board.
It's no secret the Dolphins perform worse when Landry catches more. They had Kenny Stills on that team who can take the top off the defense. They were better off throwing it to him 161 times and letting more balls fall to the ground than getting small ineffective chunks with Landry.