I get the feeling that he actually likes Bill O'Reilly in the same way we take pity on sad old men at the back of buses but that he HATES this guy with a passion.
For those who weren't following this when it first happened, the actual broadcast version of this edited out Stewart's reference to the Bill Sammons emails leaked by WikiLeaks (which directly refute Wallace's claim that there are no "marching orders" at Fox) and has never addressed this issue anywhere. This isn't surprising, of course, but it's ironic that a textbook example of exactly what Stewart was talking about should happened as he's talking to the very interview he was giving.
I don't even care what happens or who says what, the fact that Fox News pundits consider a Comedy Central employee to be their journalism Boss Fight is hilarious.