Who said anything about forcing Apple to do anything? The blog post wasn't talking about suing Apple or asking the government to step in. It was merely criticizing a system they find slimy and contrary to the interests of Apple's customers.
It isn't like Apple is going out of their way to tell potential customers "people are out there writing software that you would like to have on your phone, but we aren't going to let you have it".
Why shouldn't the EFF be free to criticize whoever they want?
It's quite simple -- you can choose not to read blog posts that are clearly going to be critical of the app store.