I disagree. It's not about the ads directly really. It's about the fact that the ads will dictate the fate of the service. To survive, the service has to go where the customers (which are not the users, but the companies buying ad space) wants it to be. Just look at Twitter: in order to monetize, they will eventually block third party apps from using the service, which is bad for the users, because Twitter's own apps can't compete with many top third party apps.
Looking at the users that are currently using the alpha version you can see that these are mostly tech people - developers, designers, bloggers, artists etc - who are enjoying even the current state, which just has a few hundred users. We don't really mind if the service doesn't scale as Twitter does, that might actually be a good thing. And there are services that proof that paid accounts are a valid and successful way to monetize: look at pinboard.in, for example.
To survive, the service has to go where the customers (which are not the users, but the companies buying ad space) wants it to be.
That is not entirely accurate either. In order to have any customers, even by your definition, twitter must continue to have lots of users. So there is already a checks and balance system of sorts in place such that if twitter goes too far in the direction of addressing advertisers while hurting the users, the users may jump ship causing the advertisers to do the same as well.
The vast majority of Twitter users today use the web interface or Twitter's own apps. These are ordinary people, not tech geeks. They don't care about APIs - they don't even know what that is. Twitter doesn't hurt them by restricting their service to their own apps. It's pretty unlikely that these people will ever want to pay $50 a year for a micro messaging service like app.net or care enough about not being a product, so they will never be the focus of app.net.
Twitter enjoys a tremendous popularity because of all those celebrities using the service. I mean celebrities like Ashton Kutcher, not like John Gruber. And that keeps the masses coming to Twitter. It does turn away the tech folks though, the people who used Twitter in its very beginning and which are now turned away by its politics.
Looking at the users that are currently using the alpha version you can see that these are mostly tech people - developers, designers, bloggers, artists etc - who are enjoying even the current state, which just has a few hundred users. We don't really mind if the service doesn't scale as Twitter does, that might actually be a good thing. And there are services that proof that paid accounts are a valid and successful way to monetize: look at pinboard.in, for example.