If he was that popular and progressives that numerous he wouldn’t have lost his primary

Propaganda works. You can bombard people with media attacks on a progressive politician to trick people into thinking he's reactionary. In this case, a heavily Jewish district was flooded with "Jamaal Bowman is antisemetic" messaging for months straight and it cost him the election.

This has nothing to do with his popularity or his progressive bonafides and everything to do with his cash on hand to run counter-programming.