The sign has nothing to do with the charge itself. It is just a convention. Just because we write an electron's charge as $-1.6\times10^{-19}$, it does not make the electron negative or its charge to be less than that of a proton.

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. In this code of communication, the proton and the electron have the same amount of charge. This is just my personal opinion but I do believe that this is far more common than the way you have expressed.

Saying that the charge on a proton is $3.2\times 10^{-19} C$ more than a charge on an electron — even though numerically correct — is not really useful as it does not convey:

1. the magnitude of the charge on the proton
2. the magnitude of the charge on the electron
3. the type of charge on the proton
4. the type of charge on the electron
5. it does not even tell if the magnitude of charge on proton is more or less or the same to that of an electron

Moreover, it could be misleading. Many of us are used to refering to magnitudes of charges while comparing their size. The idea of treating the magnitude of charges with their signs while comparing them isn't really useful.