The risk associated with high altitude radiation is far less apparent than the risk involved in the unlikely event of a depressurisation.
At FL400, a passenger has a Time of Useful Consciousness of only 30 seconds, a pilot at that altitude has only 20 seconds. At FL450 this reduces to 20 seconds and 15 seconds, respectively. Factor into this the notion that passengers will only be using a 'continuous flow' oxygen mask, which isn't at all efficient at that altitude. At that altitude, one must breathe PURE oxygen... not recycled air from the lungs.
Furthermore, above 40,000ft even breathing PURE oxygen does not provide that blood with sufficient oxygen, due to the lower partial pressure at that altitude. Special 'pressure demand' masks are required to deliver 100% oxygen at an increased pressure... and only the pilots will/should have these. This isn't even considering the fact that during an emergency oxygen intake can increase by a factor of twenty or so.
While radiation is certainly an issue for pilots at those altitudes over the course of a lifetime, the effects on passengers are negligable. That said, the most serious risk at these altitudes remains to be the rather improbable likelihood of a depressurisation.