I think it's clearly implied that profit per employee would be far preferable, but in the absence of good profit data, they're saying that revenue per employee is vastly more useful in judging a business from a business viability standpoint than, say, users, or even users/employee.

If the startup's goal is solely to be acquired, then users might be appropriate, but 37Signals has always argued that that goal is generally foolish, and akin to playing the lottery. Their mantra has been that startups should be trying to build a business, not an acquisition target.