Net Winnings are calculated as your total winnings minus the entry fees for the tournaments that you've won.
For example, if you played ten tournaments with an entry fee of $3 and won five of them for $10 each, your Net Winnings would be $35. That is, your total winnings ($50 or five times $10) minus the Entry Fees for the games won ($15 or five times $3).
Entry fees for cash games in which a cash prize wasn't awarded are not calculated in the player's Net Winnings.