Not being a lawyer, I don't know all the ramifications but in practical terms I would agree with you that there is nothing stopping a bus operator running a service at a loss, over a prolonged period of time if they so wish. You could say that by running another service at a profit that cross-subsidises the loss-making one, but I would think any QC worth his/her salt could demolish that argument. The bus company could, in theory, run each and every route at a loss: don't forget Starbucks UK managed their huge expansion while never making a taxable profit, and this position was accepted by HMRC!
There are a number of angles to this.
Firstly, while it's perhaps better to by-pass the Starbucks thing, why would any company want to provide goods or services at a long term loss? Companies have a duty to their shareholders, and even if those shareholders are accepting a 'break even' position, some operating surplus is needed to renew the fleet and cover for unexpected situations.
The remaining council owned bus companies are in a slightly different position - they are not allowed to be bailed out on a regular basis by their 'arms length' owning councils. I don't think any council has yet had the book thrown at them, and I think it's accepted if they make a small loss one year (which is an occupational risk of aiming at 'break even' - some municipals had aimed at break even and had a loss when the economic you-know-what hit the fan a few years back.)
You can drive yourself mad trying to analyse the profit / loss of every single mile of route. While there's little commercial point in running journeys that are regularly completely empty, there are the peak / off peak journey angles to consider (is a 'loss making' journey in the off peak direction that carries a few passengers really loss making if the same vehicle's peak direction journey makes enough profit to cover the out and return?)
The way the whole thing is costed is open to many variables. Since you won't ever run all your buses 24/7, most operators seek to cover the standing costs (e.g. garaging, purchase, finance / depreciation) of their vehicles over the times they can be sure the bus will be operating - say 0800 to 1800 Monday to Saturday - if the vehicle runs outside those times and covers its basic operating costs, it's probably worth doing.
(obviously the sums are different if the vehicle's primary thing is school bus runs or wedding hires)
There is also an increasing realisation that having early morning / evening journeys does encourage more people to buy weekly tickets etc, and that if a shift worker can't get to work on early turn / home on late turn because buses only run 0800 to 1800, that person probably won't make the other journey by bus.
The idea of intentional loss making is more rooted in competition law / regulations rather than transport act - broadly speaking, any business that indulges in 'predatory pricing' - intentionally selling very cheap (at a loss) to drive a competitor out of business, stands to be investigated by competition authorities. (the most blatant example was in Darlington where a certain plc blew the municipal owned operator out of the water by running free buses for a while.)