Yeah, I think that's about right. I had a pro haul long distance earlier this year and it was about $1 per loaded mile per horse. For a specialty trip to just go out and pick up a couple horses (versus a route where horses are being picked up and dropped off along the way) I can see why you were charged for the unloaded miles as well.
I am assuming this was a professional shipper? If it was a "regular person", they can't legally do that. That is considered hauling commercially which means they must abide by ALL commercial vehicle rules and regs (weigh stations, vehicle inspections, log books, fuel and road use taxes, DOT numbers, etc). It also means that unless they have commercial insurance on their truck and trailer, should anything happen while your horse is in their care, they are not covered by their insurance.
So, for those of you that charge people for hauling their horses, think about this. If you haul my $15K horse in your personal trailer and you charge me to do so, you better hope nothing happens to my horse. It is one thing to split fuel. It is another thing to charge to haul the horse.
We have 2 rigs. A deisel dually and 3 horse slant with dressing room. And a Freightliner FL60 crewcab with 5 horse head to head/mid-tack/living quarters that is 68' from nose to back. When diesel was $3.70-3.80 a gallon it cost us $0.60/mile to run either rig, loaded or empty.
So if you read my post above, unless you are paying a commercial hauler $1/mile, you are probably overpaying. Offer to buy their fuel, lunch, etc. THAT is legit (well, actually that stretches it too but it is "more legal")