Cat doors are very common over here since most cats are indoor/outdoor cats, and most cats have no problem at all with them. Of course, some prefer their human slaves to get up and open the door for them, but that doesn't mean they don't know how to use them
If yours don't get the hang of it straight away try propping the door open until they get used to going in and out of it, then gradually close it so that they have to open it themselves. Standing the other side of it with a treat also encourages them to use it. I've always used litter trays with a cover and cat door and none have had a problem using the door.
Some cats need to be shown how to use it, you can do this by picking up the cat and putting them through it a couple of times (this only works if the cat is being co-operative, don't force the issue if they are resisting with legs planted either side of the flap!) or you can stick your hand through holding a treat while they are on the other side of the door, then hold the flap open while they follow your hand through to get the treat.