Shake it from the side and a little above the tree so the hive falls to the opposite side. That way it has to fly around the tree. Run up (if you can) and make sure your net is the only tool in your inventory. Select it with the D-pad so it's the first thing that comes out, and it'll automatically have you face down. By the time you see the bees coming from the bottom of the screen, you'll already be facing down and will have your net out. At that point it's all timing.
Pretty much what the person above said.. >.< make sure you have a net ready in your pocket and when you see the bee hive fall out, run up North. Always North. When there's some distance between you and the bees, open up your bag (press x) and hold the net. You'll be facing down and you just have to time it right. Good luck!!
I think having a silver/gold net helps as they're bigger (?)
MorningStar pretty much said it all already, but just shake the tree, run, quickly get out your net, turn around and catch that bee! It can be a little difficult though, good luck!
1. Shake tree, drop bees.
2. Run directly North, until the bees no longer show on your screen.
3. Open your inventory - the bees do nothing while you are "paused."
4. Equip your net - this automatically faces you south.
5. Swing your net as soon as they appear on the bottom of your screen.