Why was the task of governing such a difficult one for President Washington and Congress?

President Washington had no precedent for being president.  However, the Constitution was carefully organized to regulate powers between the various branches of government, and those in whatever governmental office respected that. Members of Congress also respected Washington and all he had done to the point that no one, and no political party, opposed him. On the surface, then, it would appear that governance should have proceeded smoothly.  However, everyone felt that this second government of the new nation had better work, since the failure of the Articles of Confederation. The British were still capable of "rejoining the wayward colonies," and the deteriorating political conditions in France made the strongest ally a potential new external threat.

In addition to foreign affairs, the pressing domestic issue was not that the Federal Government had no means of collecting tax revenue; the issue was there was no revenue to collect!  The War for Independence had cost not only blood, but treasure, which had been freely given to the cause, but few had much in the way of money after the war was won.  Congress assumed each state's war debt, and struggled to repay it.

Finally, Washington, along with the rest of the nascent Federal Government, set up shop in New York City, then Philadelphia, and then finally, Washington, DC.  Moving, especially in those times, must have made governing even more difficult.