Claiming that the federal government has spent too much money for too long on the nation's rail system, the president of Trailways Inc., the bus company, yesterday made a detailed plea for federal aid to build downtown transportation facilities in major cities.

J. Kevin Murphy told a selected group of administrative and congressional representatives here that the was a "gross discrimination" to bus current federal transportation policy passengers.

"Bus companies, which receive no federal subsidy, must compete with subsidized transportation, Amtrak and airlines," Murphy said. While federal subsidies help out in the construction of airline and train facilities, he said, bus companies get no such aid.

Murphy pointed out that 340 million passengers travel by bus every year, as opposed to 20 million on Amtrak and 220 million who travel by air.

He also said that the intercity bus industry is the least polluting and most fuel efficient mode of transportation, yet still receives no federal funding.

He said that bus passengers are mostly the young, the old, the poor and the minorities, and they depend on buses as their major form of transportation.

"These people deserve much more than they are presently getting. They deserve to have services and facilities equal to those at regional airports, which are use primarily by the upper and middle income passengers," Murphy said.

He said his proposal for transportation centers in inner cities that would merge all forms of ground transportation would give "a pleasant environment for travelers," and help in the "revitalization of downtown areas, decrease in traffic congestion, creation of jobs and pride to a community."

He said the centers could be funded with federal aid and operated by the city of by regional transportation authorities. "Tenants of the center would pay rents and user fees to repay the building construction costs and provide operating expenses," said a press release distributed at the announcement.

"Our proposal," Murphy said, "is completely consistent and in support of President Carter's policies of zero based budgeting and job creation through needed public works.