This is just historical. For some reason one has defined what's now known to be carried by protons as the positive charge. There is a lot of confusion in the literature, talking about "technical direction of current" vs. "real direction of current" and similar gibberish.
It's way easier to just use the vector-field concept to understand these issues. The best is to use even relativistic four-dimensional notation right away. E.g., the electric four-current of a fluid with number density [itex]n_0[/itex] of charge carriers is given by
[tex]j^{\mu}=q n_0 u^{\mu}=q n_0 \gamma \begin{pmatrix}c \\ \vec{v} \end{pmatrix}, \quad \gamma=\frac{1}{\sqrt{1-\vec{v}^2/c^2}}.[/tex]
Here, [itex]q[/itex] is the charge of one particle ([itex]+e >0[/itex] for protons, [itex]-e<0[/itex] for electrons), [itex]c[/itex] the speed of light, [itex]n_0[/itex] the density of the fluid as measured in the local rest frame of the fluid cell, and [itex]\vec{v}[/itex] the flow-velocity field.
The sign of the total current through a cross section then is uniquely defined by the spatial components of this current-density vector and the orientation of the cross-sectional area:
[tex]I=\int_{A} \mathrm{d}^2 \vec{A} \cdot \vec{j}.[/tex]