The only thing certain about airline fees is that they only go up. The recent hike of legacy carrier change fees has gotten a lot of press, including on this site. However, Frontier Airlines, which has kept change fees at $100, has been quietly instituting new fees of their own.

Frontier’s policy changes that go with these fees could end up the most far-reaching of all.

The first fee is for carry-on bags. Anything that doesn’t fit underneath the seat is subject to a $25 fee, if paid at time of online check-in, and a $100 fee if paid at the airport.

Charging for carry-ons makes a certain amount of sense as far as speeding up boarding. The new twist here is that the fees only apply to travelers who have booked through travel agents or any third-party site.

As at most airlines, Elite level frequent fliers will be exempt from the baggage fees, but Frontier will also exempt passengers who book directly on “,” the airline website. (Note: Passengers booking directly with Frontier by phone will still pay the fees.)

Frontier is also cutting the frequent flyer miles passengers accrue when they book through a third party, down to 25 percent of actual mileage. (They cut it to 50 percent in September, 2012.) So now, a 2,000-mile roundtrip booked through a travel agency or online agency will only net passengers 500 miles.

Also as of last fall, Frontier only allows passengers to choose seats in advance when they book directly on the the airline website.

While they’re at it, Frontier has also decided to charge for soft drinks and bottled water, with an exemption for elite travelers and those on higher fares. (This is going to be interesting for flight attendants trying to figure out who qualifies, but that’s another post.)

Frontier doesn’t primarily cater to business travelers and, with a limited route structure, these changes are attracting much less press than if a major carrier tried them.

On the other hand, infrequent travelers may not care much about mileage and they may expect airline seat assignments. But they will definitely notice the carry-on bag surcharges.

Presumably, agents will divulge the new system up front. This could open up a whole new set of issues — do agents offer to do the finding work for a fee, then let the traveler book direct?

Some agents might try to start booking on the Frontier site instead of their agency computer? (This is more complicated than it sounds, as schedule changes, etc., may not get communicated after booking. Plus, it increases the chance for error in booking through an extra system.

So far, most major carriers trying to lure travelers to their websites have been using a carrot rather than a stick approach. United, for example, has offered some bonus miles every now and then for online bookings. Airlines offer baggage discounts and bonus miles through various credit cards, but qualifying travel can be booked direct or with an agency.

But since nothing is certain in the airline industry but change, my sense is that Frontier will either eventually give up these changes or see them spread. But we shall see.