I don't think that closed-source non multi platform games are too big of a problem. A lot of these games use sdl. One of the games in the new bundle uses unity which is closed source and was ported to linux recently(expect to see a lot more unity games in the humble bundle as unity is pretty popular especially for smaller/indie games). A number of others use XNA for which there is an unfortunately unfinished open source clone version called MonoGame.
A bigger problem is developer effort/binary testing on linux. One guy ported 9 of the humble bundle games to linux by himself(http://en.wikipedia.org/wiki/Ryan_C._Gordon#Humble_Indie_Bun... including Aquaria).
I believe Ryan/icculus did most of the porting work as well as fixing any bugs filled on his bugzilla(https://bugzilla.icculus.org/query.cgi If you see any unreported, please report) by himself. While he is a good developer that is a lot to take on for one person.
Even more importantly many games are rushed and released/ready just before (or even a bit after humble bundle release). Even "just" recompiling for a new os with the same cross platform code requires binary testing to help find unexpected problems. A number of these bugs are eventually fixed but not all of them.
A bigger problem is developer effort/binary testing on linux. One guy ported 9 of the humble bundle games to linux by himself(http://en.wikipedia.org/wiki/Ryan_C._Gordon#Humble_Indie_Bun... including Aquaria). I believe Ryan/icculus did most of the porting work as well as fixing any bugs filled on his bugzilla(https://bugzilla.icculus.org/query.cgi If you see any unreported, please report) by himself. While he is a good developer that is a lot to take on for one person.
Even more importantly many games are rushed and released/ready just before (or even a bit after humble bundle release). Even "just" recompiling for a new os with the same cross platform code requires binary testing to help find unexpected problems. A number of these bugs are eventually fixed but not all of them.