Pure water is very weakly dissociated, meaning that the amount of H+ and OH- is very small. If we look at the autoprotolysis equilibrium of water
$$\ce{H2O <=> H+ + OH-}$$
and its autoprotolysis constant at 25 °C
$$\ce{K_w = [H+][OH-] = 1.01\times10^{-14}}$$
According to the equation above we know that the H+ and OH- are the same, so we can easily calculate that the concentration of H+ is around $\ce{1.005\times10^{-7}}$ mol/L
Now let's assume you add a small amount of a strong acid, such as HCl, so that the concentration of this acid solution is 0.001 mol/L. If we assume a complete dissociation of HCl according to the following equation
$$\ce{HCl -> H+ + Cl-}$$
we know that the concentrations of H+ and Cl- ions are the same, and equal to 0.001 or $\ce{1.0\times10^{-3}}$ mol/L. Thus, several orders of magnitude higher than the amount of H+ ions coming from water.
So when calculating the pH we can use only the concentration of H+ from HCl dissociation, where $\ce{pH = -log_{10}(1.0\times10^{-3}) = 3}$. Or you can sum up the concentration of H+ coming from HCl and $\ce{H2O}$, where $\ce{pH = -log_{10}(1.0\times10^{-3} + 1.005\times10^{-7}}) \approx 3$ or more specifically 2.99996. But of course, this amount of decimal numbers makes no sense.