Because if that investigation was followed to its logical conclusion it would discredit, not only President Clinton, but the Republicans as well.
Whitewater leads directly to the Iran-Contra money laundering operation.
When Oliver North was secretly selling TOW missiles Iran at inflated prices back in 1986, the profit was used to buy arms for the Nicaraguan Contra rebels. This resupply operation was run out of a secret airfield near Mena, Arkansas. Bill Clinton was Governor of Arkansas at that time. He allegedly knew about, and protected this secret operation. After flying the supplies down to the Contra rebels, the planes returned with dufflebags full of cash which were airdropped onto farms in Arkansas.