'smith' - as you and 'ocean' have said, there are far too many variables. Lease rates for 737s vary from cheap to horrendous depending on the type and the deal you have struck. Maybe, like Ryanair, the a/c has been bought 'at a good price'. Maintenance, crew and fuel costs will not vary much between operators in terms of how the overall costs arrive.
As you say, not all seats are at £29.99. Perhaps the return flight is 'stuffed' with high-price tickets. Maybe, as 'WJ' says, for a charter airline, the 'series' of flights is paid for regardless of loads. For a holiday company's airline, the costs will be built into the holiday. For a scheduled airline, it may be a 'loss-leader' route or a 'start-up' which will almost certainly run at a loss for a while.