I had the same problem when I first started. The left stick and right stick felt the wrong way round in my head. I felt that my natural gameplay style better suited pitch and roll on the right stick and yaw on the left stick.
When I went through to re-map, because I knew it was possible, I suddenly appreciated quite how many intricate functions are mapped into the various key combinations.
It scared me....
I resolved to go back and learn the controls, as recommended by FDev.
I am getting better. I still sometimes roll when I want to pitch while docking but thankfully, I haven't yet crashed / blown-up / upset the locals to the extent that I die.
Muscle memory is kicking in now and I am starting to get a handle on what my ship is doing.