Under reasonable conditions, at any given moment, only a tiny fraction of water molecules are dissociated into the ${\rm H}^+$ and ${\rm OH}^{-}$ ions. Therefore, the molar concentrations of these ions are very small numbers, so their logarithms are negative. The customary definition of pH takes this into account.
If we add acid to water, then ${\rm H}^+$ ions' concentration grows by orders of magnitude, but still there are way fewer ${\rm H}^+$ ions than water molecules, and the concentration of ${\rm H}^+$ ions still remains a small number. So the logarithm of ${\rm H}^+$ ions' concentration remains negative in the vast majority of situations, and the pH definition still works as intended, stripping the minus sign of the logarithm.