I'm not entirely sure, but I think the automatic trading captains sort of "learn" from you what kind of profit margins you're going for.
Also, IIRC, if there's no better option to sell that meat before the trade route ends, captain will sell it for that 5 bucks more.
Might also be that his trading experience is just a little too small. Give it some time until he gets better, maybe full functionality will be reached.
Failing all that you just picked a crappy route. Yes, that can happen, too.
Personally I ALWAYS use the same route. In the parentheses is what I'm producing there (later):
Port Royale (Meat, Ropes)
Cayman (Cocoa, Cotton)
Cancun (Coffee, Sugar)
Havannah (Clothes, Rum)
Charlestowne (Dye, Corn)
Turk Island (Wheat, Fruit)
Isabella (Bricks, Wood)
Santiago (Tobacco, Hemp)
First Captain that can automatic trade gets this route assigned, second one same route in the opposite direction. Since it contains ALL the goods of the game there will always be profit. I stick to that route in the beginning of the game so I can pull up my own industry in those cities asap (build up "Trade success"). Might be a quicker way to do it, with more goods in some places, but I like it that I only got 2 goods in each town. Keeps everything manageable.
Once I got my industry up, I get two convoys with automated trade routes. Usually each of those is 10 of the biggest cargo ships. I assign the first two captains I had to those, since they tend to have the most trade experience. Actually, one of those convoys doesnt need experience all (the collector convoy, that is).
Before I start explaining how the convoys work, I'll explain how you have to set up your warehouses:
Each warehouse on those islands sells woods and bricks to a minimum of 60, price doesnt really matter, this serves a different purpose
Make sure you check "protect minimum amount from trade routes". Or however it is called in english.
Each warehouse that needs ANYTHING for production gets the same trick applied to whatever resource they need, be it corn, hemp, sugar, cotton or just tools. The minimum amount, however, tends to be around 120. (Except tools, but it all depends on the volume of your production.)
In Port Royale you set the warehouse to buy spice, wine and tools to a maximum amount of... let's say 120, at a reasonable price. (I try to stay below 600).
Now let's talk about the convoys:
The collector convoy just follows the route and you set it to load AND unload the maximum of every possible good in the according city. Means: woods, bricks and whatever that city is producing and ALSO the resources that city needs. Remember, minimum stocks are protected. Also the "unload" order always gets executed first. That way you can make sure the cities are ALWAYS stocked with the right amount of resources/building materials. I also forbid every other good for trading on the collector convoy. Yes, that convoy will therefore cost you quite some money to run, but it MORE than works out in the end.
Oh, and once the convoy reaches Port Royale again, it unloads EVERYTHING it has and then loads up 120 of wood/bricks/tools.
You dont need to load sugar/cotton/hemp/corn iirc, because the order of the cities makes sure the producing governor towns ARE already stocked with resources.
The distributor convoy:
Load up, lets say 100 of each good, for a start, in the warehouse of port royale and distribute it to the cities in the mentioned trade route. MAKE SURE tools are on auto trade, you dont want to touch your stocks of tools. You NEED that for production
The ideal amount of goods it should return with to port royale would be 1 of each, btw. Depending on the amount of production facilities you have you might notice you're producing more than those cities can use up. In that case you just create another distributor convoy that sells stuff to other cities.
Soon you will be swimming in money, so much that every crewman can wipe his arse with gold coins, should he choose to.