I've been a professor's assistant for embedded systems classes at my local university for the last few years. One of the most common problems the students seem to have when using the Saleae analyzers is that they accidentally run and then try to debug the simulation mode. (The second most common problem is having the connectors plugged in upside-down.)
Although it's pretty comical to have a frustrated student come grumbling about how everything they do ends up funky, and you point out that they don't have the USB connected, it is surprisingly easy to forget and run the software unintentionally in simulation mode.
Personally I would prefer to have the software default to unusable if a device isn't connected. This would seem to be a more typical behavior for the type of software.
Perhaps the simulation could be launched from a help menu item as a demonstration/learning tool.