Ticket prices and toilets top the list of rail passenger gripes, according to a survey of more than 3,000 travellers.
Passenger Focus found value for money was the area of greatest concern, while the service from train staff was the most highly praised aspect of travel.
Commuters were the unhappiest travellers, followed by those on business trips, the watchdog added.
The Association of Train Operating Companies said customer satisfaction levels were at a record high.
The Passenger Focus survey asked people about 31 different aspects of train travel, including cleanliness of trains and stations, availability of journey information, car parking facilities and personal security.
'Europe's highest fares'
On average, commuters felt their expectations were being met in just six of those areas, and for business travellers the figure was less than half.
Those taking trips for pleasure were the happiest, with their expectations met or exceeded in two-thirds of cases.
Fares and the complexity of the ticketing system prompted many complaints, as did shortages of seats and the way that train companies deal with delays.
But commuters were happy with the length of time their journeys were scheduled to take, with speed of travel exceeding expectations.
Passenger Focus rail director Ashwin Kumar said: "We know that commuter fares are the most expensive in Europe, with an annual season ticket for a journey such as Warrington to Manchester costing 60% more than an equivalent journey into Paris.
"Long-distance fares are complex and confusing and passengers find it hard to know whether they've got the cheapest fare for their journey.
"Constantly working to make rail punctual, good value and frequent is vital to keeping existing passengers happy and attracting new ones."
A spokesman for the Association of Train Operating Companies said customers' wants and needs were well understood.
"But operators will continue to work hard with the rest of the industry, including Passenger Focus, to improve services even further," he said.
"Train companies are under an obligation to sell passengers the most appropriate ticket for their journey and four out of five customers travel on discounted fares, suggesting that most people have no problem getting the right ticket for them.
"The average price paid for a single journey is under £5."
But Gerry Doherty, leader of the Transport Salaried Staffs' Association union, said the survey showed passengers were "fed up with being ripped off".
"[Transport Secretary] Philip Hammond should reject the siren calls from the private operating companies who want him to allow them to push up fares by 10% from January," he said.
"What he should do is to implement the Lib Dem manifesto commitment and limit fare rises in January to 1% above the RPI inflation rate. This would mean a 4% rise in the new year."