In short, Caesar was already refusing to stand down as governor and disband his army despite an order from Rome to do so; the crossing of the Rubicon was particularly egregious because Caesar left the province of which he was governor (Gaul, including Cisalpine Gaul, which we consider north Italy) with troops (the XIII Gemina) and entered Italy. He did not have the authority to do so, so by moving troops out of his province and into Italy, he was effectively (and, in the end, quite truly) launching a coup d'etat. Caesar is not the first Roman general to have done so; you'll want to note for the purposes of the class that there was a very bloody precedent for this in the actions of Lucius Cornelius Sulla, and Pompey had more or less threatened to do the equivalent when he insisted on bringing troops to Italy under the guise of waiting for a triumph, but unofficially for the purpose of pressuring the Senate to ratify his settlements in the East.