Q:

Are air marshals on every flight?

These guys say (in the discussion) that they were the only three passengers on board.
Does that mean that there was no Air Marshal on board (or one of them was?).
Aren't air marshals present on every flight?

A:

The exact number of air marshals is not public information, and they certainly don't disclose what flights they fly on or other operational details. However, the number has been reported to be on the order of ~3,000-4,000 and reports indicate the number has decreased somewhat since then. All of them are, of course, not on duty 24/7/365. There are around 87,000 flights a day in the US alone, but only around 28,000 are commercial passenger flights, where air marshals are presumably most likely (hopefully there's not a need for air marshals on military flights, for instance).
So for some back of the envelope math, let's conservatively say there are 3,500 air marshals who all work five days a week, they all work alone (in reality, they appear to work at least in pairs), and they somehow manage to average protecting four flights a day. Even with these conservative assumptions, that would only be 5000 flights/day covered by air marshals. From this, it should be clear that there cannot possibly be an air marshal on every commercial flight in the US.
The President of the Air Marshal Association/CWA (their union), not entirely a disinterested party, agrees:

"There are around 30,000 commercial flights per day over the U.S.," says Casaretti. "If you were to attempt to place a team of just two FAMs on each flight, it would require an agency of over 75,000 FAMs (accounting for training and days off). FAMs cover a very small percentage of commercial flights."
Which flight air marshals get on is determined by a computer program that assesses the probability of threat based on the aircraft, departure and destination cities, as well as the amount of fuel on board. This is the threat matrix that comes out of the missions operation center.
The TSA will not release statistics on the number of air marshals. TSA's Pascarella acknowledges only "many thousands." But Biles estimates that there are approximately 3,300 FAMs and of those, 34% are filling ground assignments in training, operations and management.
"We call them 'chair marshals,' riding out their career in management," says Biles. That leaves 66% of the workforce to perform in-flight security duties.
"If one accounts for vacations, sick leave, medical leave and days off, some air marshals working in operations have told me that this accounts for less than one half percent of all U.S.-flagged aircraft being covered by federal air marshals," he says.

A:

Air marshalls are not on every flight. I was recently at a computer science seminar by Milind Tambe, whose research team developed the software that the Federal Air Marshal Service uses to randomly choose which flights get marshals. (It's also used for security patrols at LAX, coastguard patrols at various ports and even for anti-poaching patrols in Uganda's national parks.) Note that "randomly" doesn't mean uniformly at random: certain flights are more likely to be covered than others, depending on the perceived level of threat.  But the fact that they choose which flights get marshals clearly means that some flights don't.
For those who are interested, Prof. Tambe's website has a lot of information, including some explanatory videos.

A:

Air marshals are certainly not on every flight. With 80,000 flights daily in North America it would be nearly impossible, and most flights are low-risk. Billings, MT to Denver, CO in a Dash-8 simply isn't worth the effort to either police it or hijack it.
Higher ratios of marshals to flights will be found going into the major centers, and it likely approaches 1:1 going into the DC area.

