Transport Secretary Patrick McLoughlin said the Bexhill and Battle MP was "absolutely right" and stressed upgrades to the Thameslink line Mr Merriman uses will cause disruption but eventually lead to better services.
Thameslink came bottom of a rail passenger satisfaction survey released this week with 73% of passengers telling the Transport Focus study they were happy with services.
During transport questions in the Commons, Mr Merriman said: "This morning my train to London Bridge got me in on time.
"Would you agree with me that as well as being negative when things don't work, we should also be positive to our rail franchises when they do get it right most days?"
Mr McLoughlin replied: "I think you are absolutely right.
"What you are seeing on your line and the line that goes into London Bridge and other trains through Thameslink is a massive upgrade of some £6.5 billion.
"Obviously there will be difficulties at certain stages during the reconstruction of that line but once it is finished it will be a far superior line and it will benefit from the new trains which will come into service later this spring."
The UK's worst train stations
Rail firms should be praised if trains are on time, says Tory MP
This Edwardian station was built in the early 1900s and is operated by East Midlands Trains. 59 per cent of people surveyed said they were satisfied with the station - a low score which ranked it bottom for both cleanliness and facilities in the Passenger Focus National Passenger survey.
Birmingham New Street railway station is the largest and busiest serving Birmingham. Despite the regular flow of people, only 64% of passengers surveyed in the National Rail Passenger Survey (NRPS) are satisfied with the sation.
London Bridge railway station is a central London railway station and a London Underground complex in the London Borough of Southwark. The station is the oldest railway station in central London and one of the oldest in the world. 67% of passengers surveyed were satisfied with this station, the fourth busiest station in London.
Peterborough railway station is a major interchange serving both the north-south ECML, as well as East-West long-distance and local services. The station is managed by East Coast. Just 67% of passengers surveyed were satisfied with this station.
Crewe station was completed in 1837 and is one of the most historic railway stations in the world. Like London Bridge and Peterborough, only 67% of passengeres surveyed were happy with this station.
Gatwick Airport station provides a direct rail connection to London. The station platforms are located about 70 metres away from the airport's South Terminal. 69% of passengers surveyed were satisfied with this station.
Stockport railway station was identified as one of the ten worst category B interchange stations by a mystery shopper assessment in 2009. Despite improvements being made to the station since, it is still one of the ten worst stations with only 70% of passengers satisfied with the station.
Clapham Junction station is one of the busiest in Europe by number of trains using it with many routes from London's two busiest termini, London Waterloo and London Victoria. Only 71% of passengers surveyed were satisfied with this busy station.
Maidenhead railway station serves the town of Maidenhead, Berkshire, England. It is served by local services operated by First Great Western from London Paddington to Reading, and is also the junction for the Marlow Branch Line. The survey showed 71 per cent of respondents were satisfied with the overall quality of the station, giving it the ninth lowest satisfaction rating.
Coventry station has the PlusBus scheme where train and bus tickets can be bought together at a saving. Despite this convenient feature, only 72% of passengers surveyed were satisfied with the station.