I'd say over 50% of airline pilots commute to work and the airlines have no problem with it at all. All they care about is that you show up at your report time...thats it. Some carriers actually have clauses in their contracts which aid commuters in the event that they can't get to where they need to go in time. Commuting really shouldn't even come up in the interview and they wouldn't black list you if it did so don't worry about it.