There are many ways a person can travel and keep control over many of their costs. Is the ferry too costly for some people's budget? Probably is, as it would be for me to do every trip. I figure a round trip to Alaska with my RV, we have done 13 round trips so far by RV, costs in the neighborhood of $10,000. I burn between 1,000 and 1,200 gallons of diesel on most of the trips we have done recently. With todays cost of diesel, it is easy to see where $4,000 to $6,000 of my $10K goes.
The best way is to look at the official web site of the AMHS and plug in your information and see what you costs would be. Don't get too excited about some of the figures mentioned, as in ten years on the forum, I have never heard anyone mentioned having done a round trip out of Whittier with a 49 ft rig to Bellingham. Put the trailer on the rail barge out of Whittier and then pick it up in Everett Washington at the port. Then do the same on the return trip. Then put your 24 ft RV on the ferry and cut your cost substantially.
Just figure your own costs from where you want to get on and off, then decide it if is worth it to you. Many factors get involved, from costs, to dogs, to some people just don't like boats, or the confinement of boats. But the ferry system is the only good way to see SE Alaska, other than taking your own boat on that route. Most of the people that don't like the ferry system, for whatever reason are, for the most part, people that have never been on the Alaska Ferry system. It is not for everyone, but those that enjoy it normally describe the trip as a big part of the pleasure they got from their trip to the north country.
To some people, the Alaska Hwy is just a way to get to where they want to be, it is the destination to them, not the trip itself. I have known some residents that just consider the highway to be a long, boring dirty drive, to get finished with as soon as they can. I had a BIL living just north of Denali Park, that felt this way. They would leave home on Friday evening after work and drive straight through to Bellingham Washington arriving Sunday evening, in roughly 50 hours, and did this every trip, so far as I know. At least a dozen trips . There was the 4 of them, and 3 were licensed drivers, so they only stopped for fuel and restroom stops. He told me I was just wasting my money to take a week or two, to make that drive in our RV. But we were driving the highway for different reasons, for him it was to get to Bellingham as cheaply as possible and as quickly, for me, the trip was a big part of the summers vacation. Not a right or wrong situation, just different reasons.
So a person has to decided over and over again on a trip to/from Alaska, is the purpose to see how cheap you can do the trip or how much pleasure you can get from the trip. We all have to compromise at times. I have mentioned there have been times I have been so broke on the trips I had to stop and find work to pay for fuel and food for the remainder of the journey.