Good question. It is fundamentally just a convention. When voltage clamp papers were first being published, some people would show positive current entering the cell via ion channels (and hence being opposed by negative current being applied by the amplifier) as going up the page (i.e. positive). Other people would show it as a negative current (because that is what the amplifier actually did). The convention became to report what the amplifier did. This is because this is actually the truth. As in, if we show the current that the amplifier applied, we are truly, definitely showing what the amplifier applied. We ASSUME (or perhaps hope) that this is equal and opposite to the current flowing through ion channels, but it is never exactly accurate (and in some cases can be very far from accurate). So we stick to what we know happened, and hope it is an accurate representation of what happened at the ion channels.

Yeah, sorry about that. I had a newborn at the time.