In fact, Stewart's point wasn't entirely wrong, but he got it mixed up (I'm sure because someone else told it to him and he never really understood). What he might've been attempting to get at was the projection that if the Clinton surplus would've been maintained the deficit would've been eliminated.
But, this point is also counter-factual. The budget surplus/deficits are also very affected by macroeconomic conditions. When times are good, tax revenues are higher. This was basically what created the Clinton surplus. It is also probably the most problematic circumstance with respect to the currently rising debt.