Can you use cement to fill a boiler flue hole?

To use cement only would be difficult, since it will simply start to spill over into the flue. It may not matter, but it will only allow you to fill up the flue with so thick of a material, since it has to "mound up", no way to keep it flush with the inside of the flue. I typically use masonry cement, it is available in just add water format. That with some brick or broken block, lay cement and brick in alternating courses, this will allow the material to stand up more vertical to more effectively fill the hole. Do not try to fill the whole thing at once, do it in 2 stages, letting the first application set up overnight about 2/3rd to 3/4 filled then detail the rest in the next day.

You could fill it all they way at one time, it may just be a bit more tedious.

Do be certain the surfaces you apply the cement to is free of soot and other contaminates.