Boots tend to have a much lower vendor cost than other pieces of armor. Since most armor pieces of the same type sell for a similar amount, but boots can often be bought for cheaper than the rest of your outfit, this leads to bigger profit margins on boots over other items.
Is this always true? Absolutely not. I found a level 50 headpiece that had 20 silver profit over the boots that went with it.
Boots are definitely something you want to make sure you check when flipping armor using the Flipping Gold Guide.
In some cases, boots literally can make a 50% profit over other similar level items. You look at a wall of items that all say 2 silver XX copper, and you probably will ignore the boots in that mix. But if you were to click on them, you'd find that their initial bid potentially is far lower than the other items with the same buy out.