So if you are at sea level you will receive the same amount of Gamma, Beta etc as you will in the same spot at 41000'?
No, but that's precisely because the radiation comes from extraterrestrial sources (including the Sun). Most of the radiation is particle radiation (and most of that is protons), rather than electromagnetic, and the particles interact with the atmosphere, which diminishes their effects as one moves deeper and deeper into the atmosphere, with the least effect at sea level (or below).
Some of the radiation is electromagnetic, including the hard UV that comes from the Sun, most of which is also blocked by the atmosphere. This hard UV is a potential concern for pilots, since exposure to the short end of the spectrum may increase the risk of eye diseases such as macular degeneration. However, good sunglasses (and even some ordinary glasses) can block hard UV, and so may the windows of an aircraft. Even then, the brightness of the light at high altitude and the presence of strong light at the blue end of the spectrum might also contribute to eye disease (there's evidence that exposure to intense blue light can cause problems over time).
Anyway, all of this radiation is coming from outside the Earth. Depending on one's location, charged particles may be deflected by the Earth's own magnetic field, and both particles and electromagnetic waves are absorbed significantly by the atmosphere. Flights over the poles involve more radiation exposure because that's where the charged particles come streaming in, following the geomagnetic field (this has no effect on electromagnetic radiation, though).
I wonder from time to time about crew exposures to radiation, even though I'm not crew myself. As far as I know, there's no conclusive evidence that the extra radiation exposure produces increased morbidity or mortality among airline crews. It's something to think about and perhaps something to reduce if possible, but the risk is too small for the average crew member to worry about (there are greater risks to think about than radiation). A pilot can reduce his risk a lot more by sleeping for a full eight hours than by wearing lead underwear.