Physics is all about making the right approximations, in the hope that we can gain some actual physical insight into our problem and make verifiable predictions.
For example, say you wanted to calculate the trajectory of a cannonball that has been fired from a cannon. It would be a Sisyphean task to account for all the possible variables that could affect the motion of the cannonball: air resistance, wind, recoil of the wheels of the cannon, rotation of the ball, blemishes on the ball's surface, lift, curvature of the Earth... It's pretty much impossible to come up with a full list of things that could affect it, let alone factor those into your calculation!
But fortunately, these effects are far too small to have a real effect on whether the ball hits the target or not. So you're safe make approximations - assume the Earth is locally flat, assume you're in a vacuum, assume the ball is a sphere, and so on, in the hope of making your problem tractable. We all agree that the cannonball doesn't travel in a perfect parabola, as your sums predict, but it's pretty damn close, and we've got a grip on the interesting parts of the problem.
Aside: How do you decide what a small enough effect to ignore is? Well, we've said nothing of the fact that your instruments are
unreliable too: perhaps you hit the stopwatch a little early or late,
or your ruler changed size a little in the heat of the Sun, or you
couldn't quite locate the centre of the hole the cannonball made in
the ground. You admit that your measurement is inherently inaccurate,
as all measurements are, and make an estimate of the uncertainty in
your answer. You're damn well never going to see the effect of air
resistance on the cannonball if it's smaller than your uncertainty.
This is why scientists put so much effort into devising ever more
precise instruments - so we can measure physics on smaller and smaller
scales.
So you see, the assumption in classical electrodynamics that charge is a continuous variable is just an approximation, just like assuming the cannonball is a sphere. We all know that charges come in quanta of $e$, but if we're measuring a charge of 10 Coulombs - well, who cares about the electrons?