The sign has nothing to do with the charge itself. It is just a convention.
We could have called charge on a proton to be $-1.6\times 10^{-19} C$ and the charge on an electron to be $1.6\times 10^{-19} C$. It does not make any difference in physics. Everything will continue to work the way it should.
It is more useful to refer to the magnitudes while comparing charges. I would personally prefer to say negative $5\mu C$ is greater than positive $3\mu C$ as it conveys something useful.