The reason why the story is titled A Tale of Two Cities is because the setting of the story is in London and Paris, two great cities, in 1775. This was a time in which the American Revolution was in progress (which affected England), and the French Revolution was not far behind in progress as well (which affected France).
The French Revolution was particularly violent and cruel. The Frenchmen who were aristocratic were being pushed away by the masses, and the monarchy was to be overthrown in a few more years. Therefore, the best escape for these aristocrats was to flee to London.
Therefore, the title makes a reference to the two cities for this reason.