I just got the latest Humble Bundle (6) and I've been able to install all of the games through the Ubuntu Software Center (sweet!) with native Linux versions.
Seems that game developers have an incentive to do this since, according to my latest glance at the Humble Bundle website, Linux purchasers give much more than average ($10.13, as compared to $5.48 for Windows and $7.27 for Mac).
Developers are going to care more about total revenue and support loads. Ubuntu SC only covers the most recent HB or two - I paid for 8 different ones all of which are available via Steam on Windows. Also I don't trust Canonical much these days.
I have Steam for windows installed through wine, and haven't had many issues getting my titles which I purchased from the humble bundle running. Since many of them have linux native versions already, I don't suspect we will have any issues.