But free web services are not like free software. If your free software project suddenly gets popular, you gain resources: testers, developers and people willing to pitch in. If your free website takes off, you lose resources.
So are you willing to have native code pushed to you with no control over it? Because that's the major logistical advantage of webapps that has Enterprises trying to use them.
Untrusted native code isn't strictly necessary. There is no need for locally-run software to be in any particular form, so long as it doesn't depend on the developer's server to function.
Java bytecode is excellent precedent for what is broadly possible. There are problems with it, but most of what's missing for the end user is a better degree of convenience and control.
Actually, the iOS model isn't that great IMO. Rather than relying on verifiably safe bytecode, Apple uses a combination of TrustedBSD-based technology on the phone, and human-directed testing in their labs, in an attempt to keep native code from doing things they don't want it to.
I think this is backwards for what they're trying to achieve, and I think that's part of the reason their app review process is such a pain in the ass.
But that argument is also flawed--free software in web applications is possible through other forms of revenue generation. Advertisements, services related to the product, in-app purchases....none of those options are precluded simply because the company chooses to respect their users. In fact, those options become a lot more prevalent, since there's no longer any payment for the service. But since the users saved that money, they will probably pay more for the extras--and they'll certainly be happy that they're allowed to change the product. This will also benefit the original site, since they get the changes made by everyone else.
But free web services are not like free software. If your free software project suddenly gets popular, you gain resources: testers, developers and people willing to pitch in. If your free website takes off, you lose resources.