The problem is when you are screening lots of people, most of whom don't actually have cancer. The individual risk is low, but the population risk is high. And when we talk about cancer screening we have to think at the population level.
Also (and this is according to the XKCD chart) you'd need 50 CT head scans before you'd hit the clear statistical cancer risk.
But it's not like the whole population gets a CT scan every year, or even during their entire life. If you need one anyways, there's probably a more pressing issue that 1/50th the clearly statistical risk level.