The "tool" is, of course, the male generative organ (ahem). As one should not risk handling an edged tool ("sharp-edged tool," in the version I know) in a casual manner, one should not use a generative organ unless one is willing to face the consequences.

As with everything in "Watkin's Ale," the statement has a surface meaning which is clean and a real meaning which is really dirty: If you don't want to get pregnant... don't do that which causes you to get pregnant.