PDF is solidly in the lead as both a primary and secondary ebook format.
This does not come as much of a surprise, given the technical content that O'Reilly publishes. PDF has been the preferred format for technical books since long before the Kindle launched and clearly things haven't changed.
Coincidentally, the above chart also offers some explanation for why Amazon released their own PDF format, Kindle Print Replica. Clearly there is content that readers prefer to consume as a PDF instead of a reflowable format like Epub or Kindle.
One other detail that Joe shared today was that the computer is still the single most used reading device. It even beat out Kindles, Android tablets, and the iPad:
When given a choice, readers prefer to use their computer over any other device, with the Kindle and Android tablets coming in as distant runners up.
Note how the iPhones comes in 4th, and the iPad 5th. Those details are especially interesting when you consider how much work Apple has put into trying to turn the iPad into a textbook platform (iBooks 3.0, iBooks Author).
When given a choice readers want to use their textbooks on something other than the iPad, so I find it fascinating that Apple has so far refused to (at the very least) release iBooks for OSX. This chart suggests that there would be demand from users.