Although those costs (borrowing & subsidy) may still be a lot less than the benefit which is seen.
For instance, if the rail line allows new development to occur, new business to start, a reduction in subsidies to other services (i.e. buses), less unemployed people, etc. then it can still be well worth spending the money.
Even on the very macro level, the subsidy funds two workers being paid a total of £50,000, then (assuming that neither member of staff is being paid so they pay higher rate tax) then the government would receive back about £10,000 straight away in direct tax. Then as soon as they start to buy goods and services there would VAT which would be being paid to HMRC on certain things.
In addition as soon as they buy goods or services the companies also employ staff (who pay tax and NI) and have taxes on their profits, business premisses, etc.
If those two members of staff where also previously unemployed then they reduce the cost to the government by not needing benefits. However even if they were not unemployed then chances somewhere down the chain there would be, (i.e. someone takes job A by leaving job B which is filled by a person leaving job C, and so on until job 'n' is filled by someone who was previously unemployed) which would still result in the number of people unemployed falling.
It is also likely that the amount of tax received from all the people in that chain would also likely go up, or at the least on average go up (as most people tend to move to a job which pays better, although there are always cases of people getting jobs closer to home, taking semi retirement, etc. which buck that trend).
