There were an issue his first year, and even his second year. His failures in this 3rd year were almost entirely organizational. The Jets went all in on an expensive, proven QB at the cost of other key pieces, esp. OL. I wish we could know the counterfactual what-if, had Rodgers stayed healthy. My opinion is that he would have been a bottom half QB in the league.
The Jets just didn't fill in all the key pieces they needed for offensive success. And when their prized QB went down, young Zach got put through the wringer. He had a few games where the pieces all sort of clicked, but even then Zach was having to use his legs to keep the play alive and made several spectacular plays.
My biased (but informed) opinion is that Zach, with a good system, an above average OL, and even average WRs would outperform expectations by a mile. We'll see what happens in Denver--I hope they make some OL upgrades.