The threat of a transit strike in New York City has been staved off — for the moment, at least — but New Yorkers still have reason to worry about their public transportation system. The more than 4 million people who use the Metropolitan Transit Authority pay more to keep it running than do mass-transit users in any other place in the country. Bus and subway fare costs $1.50 a ride; add it up, and the riders pay 54 percent of the operating costs of the system, not to mention a whopping 88 percent of the operating cost of just the subways. By contrast, public transit customers in Philadelphia and Boston pay just 40 percent and 31 percent respectively. Why do New Yorkers pay so much? Blame it on the government, which has been scaling back subsidies for public transportation since the Reagan years. Today, the MTA, the largest transit provider in the Western Hemisphere, receives zero federal operating assistance. If the fare rises to $2 next year, as rumors suggest it will, riders will foot nearly 100 percent of the bill.