Tesla I'm sure felt that it was extremely important to actually hit their $49,900 target, and I'd hate to see what this thread looked like if they went over that by $5,000 or something whether supercharging was included or not... Let's assume that perhaps they will actually lose a few thoasand $ on each 40kWh model they sell. Including supercharging would increase that loss of course, but more importantly they would end up selling more 40kWh models and conversely less 60kWh and 85kWh models. This situation is very similar to the $20,000+ difference between the Roadster Sport than the base Roadster. Tesla wants to sell more sports than base Roadsters because that's the only way they can make money since it costs them much less than $20,000 to actually upgrade the base Roadster to a sport. Nobody can blame them for wanting to stay in business! At the end of the day this is all about economics, and it seems apparent that Tesla needs to sell more of the expensive models and less cheaper ones in order to keep their business viable.
All that said, the 40kWh Model S is going to be a damn good car. They hit the price they promised, it looks like it's going to be on time, and it seems like pretty much everything else they promised is there as well. You still get an amazing amount of bang for the buck out of the base model, and I'm sure that their will be many, many happy customers with all of the different trim levels. The Leaf is no Model S, it just doesn't even compare really. Tesla just had to make the more expensive grades appealing enough to tilt the balance and sell more of them. Unfortunate maybe, but completely neccessary. I'm personally not critical at all towards them for this decision. They aren't perfect of course, and it's easy to see how lack of supercharging on the base Model S could upset some people, but it's important to keep things in perspective and try to understand the big picture.