I also think maybe the question was phrased incorrectly. Battery Park City often has lower price points on their units due to the fact that CC and Taxes will be higher. This is due to the fact that BPC is a land lease and spends money making it a higher quality area to live in.
I live in BPC as well, and am willing to pay a little higher in CC and Taxes b/c I highly enjoy the fact that we have some of the best cared for land Manhattan has to offer. They plant flowers to go with the seasons, many of the buildings are the Greenest buildings in the city and the air honestly is cleaner and fresher. It's premier water living like nowhere else in the city.
That being said, it is really the only place downtown where you can still find a 1 bedroom for 400,000. So the maintenance fees are higher, but in South BPC, prices are still VERY competitive.
I wonder if you accidently phrased your question in reverse. Battery Park City condos by far have higher monthly fees than condos and co-ops in the Financial District. Battery Park City is on land lease - the Port Authority owns the land and all the buildings there must pay rent for the land. Therefore the common charges are very high. The Financial District, on the other hand, has mostly new developments with tax abatements so the combined monthly cost (real estate tax and common charges) are low.
If you truly meant to phrase your question as you did, that you find the monthly fees in the Financial District to be higher, can you let me know what particular building you are talking about?