Almost every business runs at a loss in its early stages.
Just think, before a £ is received, they have to spend out on wages & salaries, aircraft purchasing/refurbishment, advertising, a decent web presence, (in SJ's case) terminal facilities, training, printing, advance rentals, and 101 other things.
Each ticket sold includes partial recovery of these initial costs, for some years. So what happens is that the initial cash 'burn' has to be reduced as quickly as possible, and turned into profitable growth. Only then do shareholders' funds start to increase. And that's without any additional investment (like additional aircraft, personnel, training, marketing, etc).
It looks as though SJ has got off to a good start. I note that they have - quite rightly - increased their prices, and the lead in price in the new year is £1099 rather than £999 on the New York service. Best of luck to them.