I actually just finished a class on this and still have most of the documents, so let me see if I can take a crack at this one. So to discuss this a bit better a little detail has to be given about the way that Athens' navy was crewed and, as is particularly important to this question, how they were payed.

For a large part of Athens' history as a powerful city-state the method of captaining their trireme fleet was called the 'Trierarch system'. This process consisted of having one of Athens' wealthy and upstanding members of its populace to be given command of a particular ship for a year's time. During this time the Trierarch acted as both captain for his trireme, and was required to foot a not insignificant portion of the operating cost of his ship while it was under his command. Providing either funds or equipment for a trireme and its almost 200 man crew was no easy task, especially since at the end of a Trierarch's term he would also potentially be liable for any damage taken to the trireme under his care and total costs could cripple even the wealthiest of private citizens.

This continual strain on individual's funds and the lack of desire of Athens' rich citizens to willingly spend a sizable fortune to have the 'opportunity and honor' of being at sea for a year and potentially lose one's life forced a relaxing of the Trierarch system, namely by allowing Trierarchs to share in the cost of a trireme's operation and potentially hire a captain to man the ship instead of the Trierarch himself, who would have greatly preferred to stay at his farm, on dry land.

Now that we've discussed the captaining and funding of the fleet slightly, onto the crewing of the ships and how the citizen navy of Athens was not necessarily as full of citizens as one might think.
While the Athenian navy was not above conscripting citizens to crew its ships, as the Trierarch system was loosened, so too were the exact requirements of crewing one's ship and since the Trierarchs were footing most of the bill anyway, they had a suprisingly large amount of leeway with who they could crew their ships with, provided the manpower was available. This led to the hiring of professional sailors and oarsmen to crew ships whenever possible, and only relying on citizen draftees when professionals were not available or funds were tight, and indeed in dire circumstances the Athenians were not above conscripting huge numbers of their citizens, including slaves, to fill the ranks of their fleet, but the cream of the crop were still the professional sailors for hire and they wanted to be payed, promptly.

Much like their land based counterparts, professional soldiers/sailors for hire really enjoy getting payed in a timely manner, when this is not possible, or is highly in doubt, as was the case during the latter years of the Peloponnesian war their loyalty was not to some grand ideal of democracy, or even any particular city-state, but of getting payed. When the Athenians could no longer reliably pay them, they would naturally look elsewhere. Similarly drafted civilians or slaves that were stuck on a fleet were usually both only marginally skilled and had a great desire to no longer be stuck on a ship that they might later die in/drown in and would desert whenever the opportunity was available.

-Gabrielsen, Vincent. Financing the Athenian Fleet: Public Taxation and Social Relations. Baltimore: Johns Hopkins UP, 1994. Print.