First of all don't piss off your neighbors so much they suddenly declare war on you with no warning. Secondly choose less valuable but easier to defend trade routes. Thirdly, build a bigger navy and have them sitting around on alert along the trade route to intimidate.
In Alpha Centauri you could set a unit to patrol and it would follow a path. I was never a big user of that feature but I know people and the AI used it to patrol their borders for alien incursions.
The other option you have is spies. I use my spies to defend, to influence City States and to serve as diplomats, but the AI spies on me and regularly spies on each other, they get intell that so and so is building up forces to attack. If you're so worried about being attacked by some AI Civilization spy on them.
I also think if protecting trade routes is your primary concern you need to choose your Civilization and unit upgrades with more care. There is a unit upgrade for both land and sea units allowing them to see further, I always liked giving that to one or two units if possible. Air units can have increased range, this is something I always take with my interceptors. Alas I don't think air units set to intercept would automatically intercede to defend trade caravans or cargo ships from a land or sea attack.
Perhaps Firaxis will introduce a feature like patrol or escort, but in the mean time I think you have to be a better neighbor, not expand so much, help out the other Civs when they ask for it, sign some friendship agreements or if you're really concerned about being attacked out of the blue, sign some mutual defence pacts.
It isn't rocket surgery, adapt, evolve, overcome.