You're absolutely right, and for people in the same office, I'd use paper, too. But I have to collaborate with people who live far away from me, which is why I created this web version of pen and paper for myself.
The idea is that several people open the same mockup and move stuff around on the screen while they're on the phone, talking about the mockup, similar to what you would do with plain old paper when sitting next to each other.
I like that you're trying to tackle the specific problem of real-time remote collaboration and made a tool to address that - that's great! The difference for me is that I rarely see value in it, compared to just scanning in a quick sketch and then collecting input via IM or email, or even with getting other scanned sketches back in return.
For example, here's a quick sketch by Jason at 37signals to get across the overall layout of their new home page:
We do the "moving sketches around" way of collaborating, and it works, but it tends to be a bit slow. There are some ways to get around the slowness: plasq's skitch makes it easy to share the things on my screen with other people, for example, and sometimes we just skype psds to each other. And I'll certainly keep using those tools.
The iPhone mockup tool I've created is a very specific tool for a very specific issue I have: I'm thinking about the layout of an iPhone screen and I want to quickly throw some ideas at somebody who's far away, and let them give live input. I don't even think that the mockup tool is the best solution for that specific problem, it's just the first idea I came up with :-)
I find it useful, but I can totally see how it's not for everyone.
What I like more than anything is that you're 1) creating your own tools for collaboration and 2) trying to solve design problems. It makes me think of 37signals and how basecamp was born, and also makes me a bit jealous because I fall into the mindtrap that programmers have more fun problems that they can hack on.
The idea is that several people open the same mockup and move stuff around on the screen while they're on the phone, talking about the mockup, similar to what you would do with plain old paper when sitting next to each other.