To explain why it would be inappropriate to skip the negatives:
Scenario- The market is going up - i.e. earnings are positive all month. You have a few funds in the pool that are positive and they total $1 million. You have a few funds that for whatever reason, are in the pool with a negative value of $25,000. The amount actually invested in the market is therefore $975,000 instead of the $1,000,000 belonging to the positive funds. If the monthly return was 1% for the pool, then had it had the $1 mill invested, it should have received $10,000. But because only $975,000 was invested, the pool received $9,750 in earnings.
That isn't fair to the $1,000,000 funds- they should have gotten their full 1% return. It isn't their fault that some other donors borrowed money from the pool and had their money invested in a different pool instead of covering the shortage in this one. So the $25,000 funds pay interest to the pool (they were borrowing money after all) to the tune of $250 and the $1,000,000 funds get their $10,000 in earnings and the $25,000 borrowers PAY 1%.
In a down market, the invested funds should have lost $10,000, but only lose $9,750 so the borrowing funds actually earn $250 in interest since they saved the invested funds a bigger loss (so to speak). So in a down market the negative funds get positive earnings and the invested funds lose money.
Earnings are allocated equitably among all the funds participating in the pool. If there is no change in in the amount invested in a month, then everyone should have the same return relative to their investment. In this case 1%. Those with positive balances earn the overall return percentage, those with negative balances pay.
Another way to look at it is to think about the overall return - the 1%. The positive funds get their $10,000 ( 1% times $1,000,000) and the negatives pay their 1% (-$25,000 times 1% = -$250). The net earnings are the $10,000 - $250 = $9750 : the actual earnings on the statement.