After a couple worries about breakages on the axle of the flipper, I redesigned it to use off-the-shelf components. I used a threaded insert for plastic and a bolt as the axle. This bolt fit very easily and smoothly through my bearing. Another advantage of using the bolt is that I can adjust the flippers' height off the board by screwing the bolt in more or less.  

Additionally, for storage it is much simpler to remove the bolt and take the flipper off to avoid damage.

In future I want to use imperial bolts with a hex head. This means the attachment to the rest of the flipper mechanism can just be the negative to the hex head and the connection between those two parts can be simplified. 
First flipper design with weak axle
Flipper design with bolt axle