UA has stated that E+ upsell brought in $50 million last year and the target for 2007 is $100 Million. I don't know how that relates to profit or not but it definitely would help offset the difference due to the lower number of seats overall.

Of course since the average flight is less than 90% full there are almost always empty seats, so what is the cost of having fewer empty seats but more legroom in E+. Only UA knows that number but I am sure that extra $100 million helps in the calculation. You only "lose" revenue on those flights that would have sold those extra seats that were removed. Then throw in the reduced fuel usage due to the removal of that extra weight of the removed seats and the number get even better.

That does not even take into account the retention of flyers who stay with UA due to the availability of E+.