Despite recent figures showing one in seven trains are delayed by at least five minutes
Rail fares increase by an average of 3.1% as of today, despite punctuality falling to a 13-year low.
In what is being described as "another kick in the wallet" for passengers, the cost of many rail season tickets has risen by more than £100.
Some examples of changes to annual season ticket prices include:
- Cardiff Central - Paddington increasing £400 to £3,020
- Cardiff to Swansea increasing £52 to £1,796
- Gloucester - Birmingham increasing £130 to £4,238
- Manchester - Liverpool increasing £100 to £3,252
Transport Secretary Chris Grayling defended the rail fare increases, telling Sky News: "I don't want to see fares rise in the way they have - of course not. The reality is though that costs do rise. Wages in particular rise very sharply in the industry.
"The money can only come from one of two places - it can only came from either the taxpayer or from people who use the railways. That's just the reality."
Mr Grayling also ruled out plans for a freeze in fares, such as the one introduced for Transport for London (TfL) for 2019 by the city's mayor Sadiq Khan.
"The consequences of Sadiq Khan freezing prices is service cuts," Mr Grayling said.
"He has now got Transport for London in deep financial trouble. It's having to cut bus routes and scale back its investment programmes precisely because if you freeze fares year in, year out, it's temporarily great for passengers but you suck money out of the system.
"That means you have less money for new trains, less money for new investment, less money for new services."
Analysis by the Press Association has shown that one in seven trains was delayed by at least five minutes in 2018 - the worst performance since September 2005.
Extreme weather, errors in the launch of new timetables, industrial action and signalling failures were among the factors responsible.
Meanwhile, Labour research suggests fares have risen nearly three times faster than wages, with the party calling for prices to be frozen on the worst-performing routes.
The party's leader Jeremy Corbyn described today's rail fare increases as a "disgrace".
"Our railway system should work for the interests of everybody, not just the profits of a few," he said.
"And it's the government that has decided on this price increase."
Protests against the rail fare increases are being held across the country today.
Rail union leaders, politicians and campaigners are demonstrating outside stations including London King's Cross, Cardiff, Liverpool, Manchester, Bristol, Leeds, Norwich and Birmingham.
Bruce Williamson, from campaign group Railfuture, said: "After a terrible year of timetable chaos, passengers are being rewarded with yet another kick in the wallet."
Research by Transport Focus suggests 45% are satisfied with the value for money of rail tickets - with the watchdog questioning when the £10bn of fares contributed by passengers will be translated into more reliable services.
Robert Nisbet, regional director of industry body the Rail Delivery Group, acknowledged "nobody wants to pay more for their journey to work" but insisted money from fares is being used to "build the better railway customers want".
The rail fare changes are not bad news for everyone, with Mr Grayling announcing that child fares will be extended to 16 and 17-year-olds by September.
Meanwhile, a railcard for 26 to 30-year-olds is being rolled out nationally from lunchtime.