> Do you feel the same abuse when you download a desktop application, and it runs code?

Not if the source code is available. Other reasons for no are that it's not automatic and invisible.

> You are free to revoke your permission for any site to run javascript, but website owners are not obligated to go out of their way to provide their services to you if you choose to do so.

People don't do that enough for it to have much of an effect.