Thousands of cosmic rays do not pass through our bodies every day... They are stopped by the atmosphere.

While the atmosphere does stop the majority of cosmic rays, a fair number do get through. As an optical astronomer, cosmic ray hits on CCD cameras are a constant source of noise in my data. Fortunately, they are easy to remove during image processing provided you take more than one image of the field. Just do a google search for 'cosmic ray' and 'ccd' and you'll find a host of webpages discussing this topic.