One big problem I see with this is that all major travel booking sites (Expedia, Travelocity) prohibit automated means of obtaining search results or fares from their sites.

The author of any such tool would be a target for legal action.

That's probably the reason why the tool you mention only pulls data from one site - they most likely have permission to pull that data. Expedia and Travelocity are unlikely to grant such permission in my opinion.