The Raspberry Pi Foundation are not an open source organisation. They produce some open source software (I can't even find coherent source for the pixel desktop), but all of their boards are closed source.
Arduino had the advantage of being open source from the components up - you could make your own boards, and many did. Unfortunately, it seems that more recent models like the Yùn have broken that promise: http://www.wifi4things.com/arduino-yun-what-is-under-the-hoo...
The Atmel chip design is not a free hardware design, though. There actually are chips whose design is libre, such as the Parallax Propeller (under GPL.)
I never really fancied Arduino as a business, then came the Raspberry Pi Foundation and I found my true love.