Radiation gets absorbed by the atmospheric gases. How much radiation you encounter depends on the altitude -- how much material is above you: more material, less radiation.
People who work in jobs where they keep track of how much radiation they're exposed to at work have to be careful not to wear their radiation badges when they fly across-country. Although it's certainly not fatal, the additional radiation at high altitudes is measurable and can mess up the record-keeping.
There should be papers that were written about the radiation environment encountered by the Galileo Probe within the atmosphere. Unfortunately, so far I've only found popularizations showing the radiation it detected above the atmosphere.
See
http://spaceprojects.arc.nasa.gov/Space ... leo_probe/
.