So what are you expecting?
I was on that boat with Dandy Don last year--nice video, Don! I'm really glad we went. I have nice memories of Holbox, but there are things I would do differently if I did it again.
You can basically do Holbox two ways--make your own way, more or less, to the island and stay a night or a few, as we did, or do a day trip. Each has advantages.
We stayed two nights and left ourselves only one day for the whale shark thing. We were supposed to go with an operation that our Cozumel dive shop recommended and called on our behalf, but reservations got misunderstood/mixed up and we ended up having to go with someone else. We signed on with our Holbox hotel's operation simply because it was late in the day and we were afraid that if we didn't settle on something fast, we'd end up with nothing.
I think it's pretty easy to show up and find someone to take you out. But it probably pays to do your research AND have a solid backup plan--it seems many/most operators will let you swim 3 or 4 times, and no more--so if you have a bad turn (equipment issue, whatever), that's it. We talked to some people who went out with a captain who let them go in as many times as they wanted (within reason) until they were tired. That's what I had been hoping for. Because my snorkel valve got stuck as I hit the water on one of my 4 swim turns, I ended up really only seeing the whale shark twice for my hundred bucks (and unless you're Michael Phelps, you won't keep up with it forever). I left our boat still wanting more--although the manta was a nice bonus! On the way there we saw dolphins and scads of rays gliding by beneath the boat, and there was a pretty little jaunt through the lagoon at the end. Other things you might want to consider is how important it is to you that your captain speak your language (or vice versa). You don't need much, as the main communication may be, as it was for me, some variant of, "Lady! Lady! Lady! Go! Go! Go!" But if you like your guys chatty and/or extra-informative, do your shopping.
One thing I very much liked about our operator--no one asked that I wear a vest.
I thought the island was delightful--super laid back, and eating is heaven if your idea of a great meal is really fresh fish simply prepared. It was mine.
We took the ferry from Coz, then the bus from Playa, then the ferry to Holbox. It all worked flawlessly, though the bus isn't for everyone. If you decide to sleep on the island and it's high shark season, definitely reserve your hotel as far ahead as you can. We called three weeks ahead, and very few rooms were left on the island. We saw several groups of people wandering from hotel to hotel, hoping in vain for a bed. Late into the evening, they were still looking. For all I know they ended up sleeping on the beach.
If you just want to compare value, I think doing a day trip can end up being a fine idea--but we wanted the adventure.
So is it worth it? I think so. Will it meet your expectations? Maybe. Or, as in our case, almost. Definitely a cool experience.