If Prometheus only ended up breaking even on its budget and advertising costs, (or even losing a little) it still would be very profitable for Fox as a whole and could still warrant a sequel. As it is, it looks like they will make a decent profit on the film.
There's more to a franchise than just box office take. A film can break even on pure box office numbers but still be a financial success when taking into account product licensing, television licensing, Blu-Ray/DVD sales and video game licensing and the long term valuation of the brand. The existence of a new entry in the franchise rekindles an interest in existing franchise properties, such as the value of the existing back catalog of Alien films.
Hopefully Scott gets to make his sequel(s), but even if he didn't, the Alien franchise would still be the basis for films, television and gaming for decades to come and the very existence of Prometheus helps advertise and elevate the long term value of the franchise/brand.