Well, I don't know the dev perspective on this but most things do not readily have .ipas available. For example f.lux is an application I use all the time on my Mac. But I haven't been able to get it into my phone for a while. Couldn't find a .ipa.

Maybe developers want to be able to charge for their apps at some point in the future through the Cydia store ? Just 'cause you can't get your app into the app store doesn't mean you shouldn't make money off it if people love it :) (just speculating, maybe that's not the reason..)