Why did Washington warned not to base political parties on geography?

George Washington did not warn against the geography-based power base of any political parties, because there simply were no political parties in his day. The new United States was (as the name implies) a confederacy of geografically defined areas, so it would not even have been logical for him to be against a geography-based political system.

Today, the influence on geography on parties' power even gets bigger. Over the last years, the Republicans (mostly, whenever they got a majority in the Federal or State Congress) have sought to perpetuate their hold on States and Districts by a process called Gerrymandering. This is a process in which the geographical boundaries of voting districts are redrawn in such a way as to assure a majority of Republican voters. In a more distant past, Gerrymandering was practised by both parties, but now by all accounts it is the Republicans who are doing it nationwide today.