Fly fishing isn't necessarily difficult to learn, but once you get the hang of it you realize there's a lot going on. Casting, mending, line control, okay mend again... Wait! Did something just eat my fly? Maybe, maybe not, but if you never set the hook you'll never know. Catching is hard enough in fishing, but even harder in fly fishing. In my opinion, it is what makes the sport a challenge. It is a hand/eye and reaction time sport. If you aren't focused and quick to respond you aren't going to catch many fish.
The big difference in fly fishing is that you do not normally feel a fish bite. With the thick fly line and tapered leader any subtle take is going to be absorbed. Unlike spin fishing where you feel the fish bite a lure and turn or eat bait and begin to swim away, trout suck in flies and spit them back out in about a second or so, usually without moving much. It doesn't take them long to realize your feathers and fur isn't a real bug. Unless you are streamer fishing you won't feel it. Fishing dry flies allows you to see the fish eat, but you have to get a good hook set before the fish spit out the fly. And what do you do if you are nymph fishing? How do you know if a fish has taken your fly?
Using Strike Indicators to Help Set the Hook
Strike Indicators come in very handy to identify whether there is a take on your fly. Strike indicators (fly fishing bobbers) float along the surface and if a fish takes the fly it will usually stop, duck under the water, or move around a bit unnaturally. Strike indicators are imperative fishing nymphs unless you tight line your flies. To set the hook while nymphing keep the rod tip going with the indicator downstream, Let the fly go downstream and lift the rod tip at the end to cast again. If you see anything out of the ordinary at all set the hook and lift the rod as fast as possible. Starting with the rod tip low a solid pull up and raise the rod tip will work well enough, but you have to get the fly line tight. These aren't huge saltwater fish and they make the hooks sharp for a reason. You'll want to set the hook into the fishes mouth, but be respectful of your tippet. Same with dry fly fishing, as soon as that fish closes its mouth set the hook.
Streamer Fishing and a Good Hook Set
Fishing with streamers you will fill a tug so set the hook quickly and move the rod to the side or above you head so as to not pull the fly out of the fish's mouth. Some people prefer a strip set when fishing with streamers, and I did this a lot when I started fly fishing. I have found though that the weight of the fish and a hard set sometimes pops your tippet. It can also be hard to set the hook properly if you pull the fly away from the fish.
I Set the Hook, Now What?
A solid hook set is important, as well as keeping tension on the hook the whole time. Otherwise fish can spit the hook sometimes, and will sometimes regardless of how well you hook them. Counteract the fish's motion. If the fish is pulling upstream to the left then your rod should be over your right shoulder. The goal is to control the fish's head as it's tail can only push and accelerate . Never straight line the fish as this puts extreme pressure on your knot. I also say a good amount of pressure to catch a fish is to have enough bend in the fly rod to make a lower case "f". More bend than that and you have to give fish line, less than that it is up to you to make the rod bend that much. You can either hand land them or reel them in,
So when it comes to setting the hook, the quicker the better. If you can watch the clues and use a strike indicator you can greatly increase your catch. You are going to miss fish, that's okay. I always take solace in the thought that I got that fish to bite something in the first place so I did that right. If you think it's a bite set the hook, better to retrieve your fly out of a tree than miss that 4 pound brown trout because you weren't sure.