Binding is difficult for the new maker. My first attempt was on a guitar without a router: it took a long time and was far from perfect.
Using a router with some sort of jig or bearing that follows the side requires it to be square with the face. If not, as you have found, the rebate is not even. You can try to even it up with a chisel and flat file but that requires patience and a steady hand and you can easily make things much worse. The message here is that a mistake not corrected has consequences down the line: on your next build ensure you get the sides bent true.
If you build with a curved back and have true sides there's still an issue. The rebate will be even on the back but not the on side as the router will ride up and down as it follows the back curve. You need a jig that deals with that issue. You can buy one (expensive) or copy one of the solutions to be found on the forum (or on you tube).
Make sure you bend the binding before you try to fit it and buy decent tape to fasten it (I use the 3M scotch blue tape). If you don't bend its difficult to pull the binding tight at the waist, leaving a gap.
When you do finally get good rebates (on future ukes) with a router, it's always a good idea to dry fit binding. This will show any issues which can be carefully rectified before gluing the binding (and purfling) in place. A large flat file with one smooth edge is useful here: the smooth edge is used on the true rebate surface to guide the file whilst its cutting face corrects the problem on the other rebate surface. Being able to do this well really improves the appearance of any instrument.
Making is all about learning new skills, that's why it becomes addictive as we try to do things better and quicker in search of the perfectly made and great sounding instrument. Just keep at it and enjoy it.
