Its amazing how something so simple can be so misunderstood.
U Tubes work off a very simple siphon principle. Nothing new here. The problem is water flowing over a weir carries bubbles with it. If there isn't adequate flow through the U Tube, they can accumulate in the apex. Have enough flow, they dont.
There are other factors, Not all U Tube overflows are created equal. Some are designed very well, some are not. Because of the design differences, some are more susceptible to air accumulation than others. A U Tube overflow that would require an external vacuum pump to remove air would be a very poor unit.
How much flow is needed? The typical overflow with a 1" U Tube needs about 200 GPH minimum to keep bubbles pushed through. Not a ton of flow. A Mag3 can do it with typical head. An overflow with a smaller U Tube like 3/4" will need less.
How to increase flow? If the pump is too small, use a bigger one. Often, people use inadequate pluming. Just using a better plumbing setup will often fix the issue.
Again, use decent equipment and set it up properly and it works as designed. No different than anything else. There is always the option of a work around fix instead, but its not difficult to do it the right to begin with.