By taking the stance on Flash. If Hulu rolls out a subscription-only product for mobile devices, but still has a free version of computer access via browser, then enabled Flash would give iPad owners the option to take advantage of what should be the more convenient player associated with the subscription OR go through Safari to use the web version.
The stance against Flash promotes efforts to monetize such content. If Apple would flip flop on this, Hulu would have to either continue the ad-revenue model "as is" or force the subscription model via all delivery mediums. A pure subscription play Hulu is probably not compelling enough to win a lot of subscribers, unless it further upgrades its programming to be a real alternative to a cable/satt bill already being paid. More simply, right now Hulu is an adjunct to a cable/satt bill for many people... because Hulu is free. Make it an added cost via subscription and it needs to compete with cable/satt bills, or motivate people to just pay even more for television distribution via more mediums.
I agree with many here who see a shift of Hulu to a paid model yields a dramatic drop in Hulu users, unless Hulu can directly replace the need for money already being spent for cable/satt. But I know the latter can't happen since the cable/satt players tend to be the one's serving up the broadband through which this Internet distribution flows. Bite into too much of the cable/satt cash cow and broadband rates will simply go up to make up the difference. That's why your current TV provider is probably also your broadband provider- they're securing the monthly subscription fee from you no matter which way this might play out.