In January First Great Western (FGW) cut season ticket holder discounts payable for missing its performance targets from 10% to 7.5%.
But commuters buying monthly tickets to London this week had to pay the full amount, with no discount.
This means a Reading-Paddington passenger who paid £332 per month with tube travel throughout 2008, and £366 last month following fare rises, must now pay £398.
Samantha Lamb, 24, who works in advertising in central London, said: "I could soon be outpriced. Overcrowding has not been addressed - my £398 per month just about gets me a squashed standing spot near the loos."
One commment posted on the online FGW passenger forums said: "I renewed my ticket from London to Reading and was told that there would be no discount. So from paying £332 in December, I had to pay £398 today. This is daylight robbery."
Some commuters were being informed by ticket clerks the discounts had been scrapped altogether, but FGW told the Chronicle prices have risen because it has hit specific service targets.
Its figures show that in the past year 89.9% of high-speed services arrived within 10 minutes of scheduled times - still short of its 90% target. But FGW only offers discounts if it slips below 89%.
FGW spokesman Dan Panes said: "The discounts certainly haven't been scrapped altogether, the targets have been met.
"We've still got much to do but we're pleased we are now delivering a service much closer to what our customers want on a regular basis."
In July Reading Borough Council's powerful corporate, community and external affairs (CCEA) scrutiny panel carpeted FGW bosses and made them face public questioning on the company's performance. Councillors want them to return in the summer.
Reading East Lib Dem hopeful Gareth Epps, who commutes to London, said: "Reading commuters already pay some of the highest fares per mile in the world, so to reduce the discount it should rightly be paying for poor
performance is arrogance of the highest order."
But watchdog Passenger Focus' FGW manager Michael Greedy said: "The failure to achieve passenger charter targets prompted FGW to pay passengers above and beyond the compensation owed. Passengers tell us that punctual and reliable services are their top priority and it's only right passengers are compensated when trains are late.
"FGW has not broken the terms of its franchise agreement by now withdrawing the discount for season ticket holders as they are now achieving and exceeding the passenger charter targets. They're under no obligation to consult with passengers as this is an automatic process linked to actual performance."
l South East Green Euro-MP and party leader Caroline Lucas will join Green Party members outside Reading Station today (Thursday) to protest against high fares.