I imagine the problem with Arecibo is maintenance costs. Just maintaining the structure must cost a fortune (the dish itself is made up of wire mesh panels suspended by a latticework structure, and the receivers are suspended on cables from metal towers). In that climate, rust alone must require constant sanding and painting, not to mention servicing the delicate electronics exposed to the dampness. The sheer scale of the place is enormous too, it must entail a similar maintenance program to a major suspension bridge. I haven't been there in years, but I also suspect civilization is creeping in, the isolation required by a radio telescope may be rapidly disappearing due to simple population pressure.

The original facility was called The Arecibo Ionospheric Observatory, and it was used to study radio propagation in the atmosphere as well as astronomy. I suppose as long as that communications mission was vital, government funding was available, but for pure research, there never seems to be enough money.