Offering an alternative viewpoint. Many seem to be focused on the cost/FTE. The alternative view is that if this was a business then $3m a year to run it is "peanuts" for the services provided. In fact I prefer the for profit model. I'd like them to charge for each account/cert to cover their costs.
The whole point of Lets Encrypt is not to charge people for the certificates. But I agree that the amount they are spending per year is very modest compared to what they are doing.