I always turn it off so that I can be notified when to send out a new trade route, and as far as I can tell there's no option in the settings for it to remember my preferences or auto-disable.
Activity Newest / Oldest
Status changed to: Done
oh what the heck, I thought for sure I double checked. Lol
I think this already exists, there's an option at:
Options > Gameplay > Auto Collect Trade Routes By Default
Unless I'm misunderstanding what you mean.