Rail fares for season ticket holders have increased by an average of 4.2% as the annual price hike, announced in August, comes into effect.
Overall, ticket prices have gone up by 3.9% in England, Wales and Scotland, but rises vary between train operators.
The TUC has claimed average train fares have risen nearly three times faster than average incomes since 2008.
Transport minister Norman Baker said the government had intervened to ensure fare rises were capped at about 4%.
"Regulated" rail fare increases - which include season tickets for most commuter journeys and off-peak fares on most intercity routes - are calculated by using the Retail Prices Index (RPI) measure of inflation plus an additional percentage.
Initially the rail fare increase was set at RPI plus 3% - a total of 6.2% - but this was reduced to RPI plus 1% by the government in October to a total of about 4.2%.
Mr Baker said: "We are engaged in the biggest rail investment programme since the 19th Century and it is only right that the passenger, as well as the taxpayer, contributes towards that.
"In the longer term we are determined to reduce the cost of running the railways so that we can end the era of above-inflation fare rises," he added.
Train companies are allowed to vary regulated fares by up to 5% above, or by any amount below, the average change in regulated fares, so that they can respond to changes in demand in particular areas.
Fares that go up by more than the average must be balanced by others that rise by less than the average, or that fall.
In developments across the UK:
- In London, passengers on the Tube, buses, trams, DLR and commuter trains face on average a 4.2% increase, while some rail season tickets have gone up by much more
- An off-peak day return between Bristol and St Austell in Cornwall has risen in price from £53.10 to £75.60 - a rise of 40%
- The cost of an annual ticket from Banbury to London has risen by 5.98%, an increase of £284, according to Chiltern Railways
- An unregulated return between Birmingham and London went up by 10%, although it only adds £2.50 to the fare
- Some tickets will rise by as little as 2.3% while one ticket, from Shenfield, Essex, to London will be £16 cheaper, at £2,704, a 0.6% drop.
Meanwhile, rail fares in West Yorkshire are rising by 6.2% - more than the national average.
West Yorkshire Metro, the county's public transport provider, said the rail prices reflected the extra 3% agreed in 2006 to provide 1,700 additional seats on peak-time train services to and from Leeds.
But independent campaign group Railfuture said there was "huge frustration" among passengers in the region.
The Campaign for Better Transport (CBT) and Railfuture have both calculated that some rail fares have increased by 50% or more in the past 10 years.
CBT chief executive Stephen Joseph branded the rail fare increase "truly shocking".
He said: "The impact of successive governments' policies on rail fares is appalling.
"We have deliberately made getting the train to work an extravagance that many struggle to afford. The time has come not just to stop the rises but to reduce fares."
The group have launched a petition calling on government to end the above-inflation formula used for determining the annual rise and commit to reducing fares relative to inflation.
The TUC's Action for Rail campaign said rail passengers will be paying more for a lesser service, as rail operators begin to implement job cuts as part of plans to save £3.5bn across the rail industry by 2019.
Frances O'Grady, general secretary of the TUC and chairwoman of Action for Rail, said: "At a time when real wages are falling and household budgets are being squeezed, rail travellers are being forced to endure yet another year of inflation-busting fare increases.
"As well as having to shell out record amounts of money for their tickets, passengers also face the prospect of travelling on trains with fewer staff and having less access to ticket offices. They are being asked to pay much more for less."
The chief executive of the Association of Train Operating Companies (Atoc), Michael Roberts, said it is the government that decides how much the annual average season ticket rise will be.
"Successive governments have required train companies to increase the average price of season tickets every January since 2004 by more than inflation.
"Ministers want passengers to pay a larger share of railway running costs to reduce the contribution from taxpayers while sustaining investment in better stations, new trains and faster services," he insisted.
Labour shadow transport secretary Maria Eagle said rail fare hikes had come as a "nasty new year shock" for many commuters and accused Prime Minister David Cameron of breaking a promise that rail fares would not rise by more than 1% above inflation.
She said: "The government should come clean with commuters that this is a direct result of their decision to cave in to pressure from the private train companies to let them hike ticket prices beyond the so-called cap."
Transport 'overhaul' plea
The shadow transport secretary said Labour would "strictly enforce the fare cap on every route and restore the ban on train companies imposing higher increases".
Sustainable transport charity Sustrans has warned that train travel is becoming "increasingly unaffordable" for families and called for a "major overhaul to our transport system".
Chief executive Malcolm Shepherd said: "Many are facing a stark choice, fork out for expensive train travel, own a car and cut back on essentials, or stay put and miss out on jobs and opportunities."