The report said the overruns of engineering works was "unacceptable"
MPs have criticised the huge bonuses to be given to rail bosses despite "a catalogue of failings" on the network.
Passengers were "inconvenienced and humiliated" by three major engineering overruns at New Year, a report by the Commons transport committee said.
Three Network Rail directors are to get bonuses in excess of £200,000 each.
Chief executive Iain Coucher said the report did not reflect the "pivotal role" Network Rail had played in improving the railways.
The Department of Transport said bonuses were a company matter.
The New Year overruns, including one on the busy West Coast Main Line, had "laid bare an entire catalogue of management failings for all to see", the report stated.
The committee said that rewarding senior managers with "huge financial bonuses ... is a gesture which adds insult to injury for the long-suffering passengers who had to struggle with the consequences of the company's failings".
Thousands of rail passengers were delayed by the engineering overruns at Rugby on the West Coast line, at Liverpool Street station in London and at Glasgow Shields Junction.
The report said the management of the three projects indicated there were "serious deficiencies" and the overruns were "quite simply unacceptable".
The committee also said it was "deeply concerned" that passengers were paying a significantly larger share of the running cost of the railways.
The committee's chairman Louise Ellman said: "The railways are increasingly popular and the (government's) 30-year strategy has the potential to provide a tremendous sense of purpose and direction.
She added that the management of the new year engineering works had "provided evidence of flawed management".
A Department for Transport spokesman said: "Britain has a successful, growing railway - last year carrying over 1.2bn passengers.
"Major projects are under way or near completion. We are targeting £10bn to bring about the single biggest increase in capacity for a generation.
"Decisions on bonuses are a matter for Network Rail's independent Remuneration Committee," he added.
"Bonuses are determined against key performance indicator targets set by the independent Office of Rail Regulation."
Commenting on the report, Network Rail's chief executive Iain Coucher, who will receive a £305,000 bonus this year, said: "We are disappointed by the comments in the Transport Select Committee report which do not reflect the pivotal role Network Rail has played in turning around the railway from the mess inherited from Railtrack.
"The railway is now performing at the highest levels of punctuality ever recorded and it is passengers and freight users who are benefiting from this turnaround.
"That effort has also delivered for passengers, who have shown their confidence in us and returned to the railway in their millions," he added.
"These are the results of a successful company and we are determined to continue to build a bigger and better railway."
Liberal Democrat transport spokesman Norman Baker said: "The Government's abject failure to plan for a high-speed rail network has condemned passengers to years more misery and overcrowding."