Philadelphia had a couple of big advantages. At the time it was the largest city in the colonies, at about 35,000 people. Larger than New York or Boston. That meant it had the facilities to host a congress, including both meeting halls and lodging.

It also had the advantage of being centrally located. If you look at maps of population centers of the US, like this one you'll notice that the population center in the late 18th century was far closer to Philadelphia than New York or Boston. So it was equally convenient to Boston and Charlotte.

Philadelphia was also located near the dividing line between North and South, meaning it wasn't viewed as belonging wholly to either section.

So big, central, and neutral, it was pretty much the perfect location. After the first congress in 1774, it also became easier to meet there as it had proved to be able to host the meetings.