There's a lot of hidden costs and infrastructure needed for magical flying beasts. Not to mention limited capacity. Little can compete with the horse drawn cart when it comes to capacity for price though.
For trading, boats have always been better in regards to the amount of stuff you can carry, even back before sails were invented. Also, unlike roads, water doesn't need maintenance, it just needs to be at a high enough level that the boat won't crash into rocks or whatever.
My main point was that boats aren't free to run. They require constant maintenance and care to remain viable. If you're going to include the maintenance and running costs of a horse team, then you need to also include the equivalent for boats.
Don't get me wrong, when you have a waterway, boats still win, by a large margin. Hence why Europe has so many canals etc.
I have giant hummingbird mounts in my game, but guess what? They need nectar from giant flowers, or just barrels full of sugar water, and/or they sometimes pick fights with giant insects in order to try and eat them. (Fun fact, hummingbirds eat small insects IRL) They're dead useful and loads of fun, but it exacts its price.
I'm so very glad that I never tried to enlarge my pseudodragon familiar to try and ride him into battle. Never even thought about the fact that pseudodragons cannot pay attention for shit.
Plus, not every species can be domesticated. Gryphons and dragons are independent and not herd animals. So they may not understand the concept of following a leader, which is an important part of domestication. And if they did, you'd probably have to best them in combat before they'd do it.