In addition to what /u/LegalAction says, we know very little about Labienus. The Wikipedia article on him is pretty bad, since it basically only uses Tyrell as a source, and though he's one of the more knowledgeable sources on Labienus, Tyrell does consistently emphasize things that support his conclusion that Labienus was always a partisan of Pompey's. We know next to nothing about Labienus' life before his tribunate, but it appears that he was closely connected with both Pompey and Caesar at an early date in his career--his ascension to the tribunate in 63 appears to have been Pompey's doing. Tyrell suggested that Labienus was from Picenum and that he was therefore tied politically to Pompey, who was declared patron of the city during the Social War. But that's an argument that I, and many others, find very weak, and I'm a bit peeved that whoever wrote the Wikipedia article bought it without thinking about it at all. It displays a pretty poor sense of the way patronage and political ties worked in Rome--Cicero's fucking brother was one of the most devout Caesarians, despite Cicero's leanings in the other direction, and similar divides in political opinion are extremely common. Why would Labienus feel unduly bound to Pompey simply because Pompey was the benefactor of his town when much, much stronger bonds could and were easily broken by individuals all the time? Besides, I think Tyrell vastly overstates Labienus' connection with Pompey. Pompey got him his tribunate, but Labienus' entire career was spent working for Caesar. Labienus' two important actions as tribune were his accusation of treason against Rabirius, which was done at Caesar's request and almost certainly planned largely by Caesar (the entire affair reeks of Caesar's hand and meticulous political maneuvering, which was very unique and quite distinctive), and his motion to return pontifical appointments to the people, which secured Caesar the office of Pontifex Maximus. The only action clearly in Pompey's favor during his political career was his nomination of honors for Pompey, which everybody was fine with doing anyway. He had at least as much reason to side with Caesar as with Pompey if personal opinion is discounted and we evaluate this based purely on political ties, which is why I think Tyrell's assessment ultimately fails, though it is interesting.

Gelzer suggested that perhaps Labienus was upset that Caesar did not grant him the honors he thought he deserved, but if I remember right he discards it because there's simply no real evidence for it. In the end Gelzer concludes that Labienus probably just supported the Republican government and disapproved of what Caesar intended to do, which is what I agree with. Certainly discord was not unknown in Caesar's ranks--he appears to have had several entire legions defect to Pompey, as well as mutinies in his veterans, and a number of his supporters either defected with Labienus or got cold feet and were moved to the rear. And Labienus' son was a Republican commander under Brutus and Cassius, refusing to side with the Triumvirs, so it's possible that the belief in the Republican government was a family position

But in the end we really have no idea, we can only guess, as /u/LegalAction says. All these theories and stuff are fun and interesting, and make great ways of discussing the interaction between politics and individuals, but they don't actually tell us anything

You'll have to ask him.

Caesar march on Rome caused a huge political schism in Roman society. You can read in Cicero's letters of the time his hesitance to join either side, although he eventually committed to Pompey. A number of Senators took Caesar's side and the constitutional issues are problematic, but it's not hard to imagine someone on Caesar's staff would disagree with Caesar's constitutional reasoning for the march on Rome. This is the problem with an unwritten constitution. Both sides had legitimate arguments for their actions and there was no one competent to adjudicate the dispute.

It's also worth noting that crossing the Rubicon isn't mentioned except in passing until Lucan, around 100 years later. If I remember correctly Cicero wrote a letter to Atticus dated Jan 25 in which he expresses the hope that Caesar and Pompey can reach a negotiated solution (Cic. Ad Att. 7.14 is the letter), and that's like two weeks after Caesar is supposed to cross the Rubicon. I think Morstein-Marx has something forthcoming on this issue, if it's not published already.