When Caesar crossed the Rubicon the Senate finally realized that they had made a terrible mistake. The mistake wasn't in letting the situation get that far, but in that they believed the Roman and Italian people would rally to defend the Republican system. What they failed to understand was that the people had little trust in the Senate and that Caesar had won them over through his popular agenda while in political office. Caesar's great propaganda campaign, his books "Bellum Gallicum (the Gallic Wars)" endeared the people even more to their almost mythical hero, and the Senate's cause in Italy was lost. Unable to levy armies, or develop a meaningful resistance, the Senate, and Pompey had little choice but to take their business out of Rome and into Greece. It was here, and further east, where Pompey held considerable sway, where the Senate hoped to raise armies and defeat Caesar.
This too, however, worked in Caesar's favor. Without the fear of bloodshed and damage to their homes in Italy, the people had little reason to support the Senate. Caesar marched throughout northern Italy accepting the capitulation of cities and garnering support with little difficulty. Pompey and the Republicans, meanwhile fled to Brundisium in the heel of Italy, where they hoped to secure the bulk of the transport vessels available in the region. The bulk of Pompey's forces were removed across the Adriatic to Dyrrhachium, along with the bulk of the Senate, but by early March of 49 BC, he still had nearly 2 full legions with him in Brundisium. Caesar approached quickly with 6 legions in an attempt to put an end to the resistance then and there. Attempting to box Pompey in, Caesar tried to negotiate peace, but Pompey delayed just long enough to make good his escape. Despite Caesar's attempts to block the harbor, the Republicans controlled the navy and Pompey escaped with his forces intact.