Not all of these were developed as cross-platform from the start. AFAIK, Humble actually reaches out to game developers to help nudge along ports on other platforms for the bundles (to what extent exactly I'm unclear on).
Some time ago I purchased The Binding of Isaac which is an amazing game, but it suffered from slowdowns on my computer. I guessed that it was Flash and this was indeed the case. It’s ridiculous that a game of that style does not run properly on a modern computer. These and similar incidents have left me very wary of Wine wrappers and Flash.
http://www.doublefine.com/forums/viewthread/8612/P15/#260851