About 20 reasons. It's extremely costly. it takes special jetways, special concrete under where it taxis and parks, special boarding procedures, all kids of extra stuff. second, it's too big and flies empty a lot of the time. A lot of routes can't handle the capacity that it has and should have smaller planes. third, it's a maintenance hog. engines blowing up, wings bending and parts falling off, airplanes being taken out of service repeatedly for changes to parts to correct a design flaw. forth, though cost per seat mile is low, the overall cost is high. it burns a lot of gas, it has to have bigger space around it because it makes such a huge wake, it's a pain in the butt.
it's not a surprise that Airbus was about to quit producing it and only continued recently when they were able to sell a few at cost, or a bit below, to someone. They went quite a while with no orders because no one wanted it, Even with the price cut to the bone. Airlines are going for smaller planes flown more often on routes rather than bigger planes once in a while. That's why the 747 is going away and the A 350 is coming in.