It is actually is a combination of factors between GM/Ford vs Toyota, Honda. Some that come to mind are degree of capacity utilization of each plant (i.e. ~70% vs 100%), labor costs (Union vs non-union), how many hours it takes to build a car (Toyota's average about 40 hours, the big 3 were up to 60 until a few years ago, getting much better now) and so on.
But at the end of the day, GM / Ford sticker prices for comparable cars have traditionally been cheaper than Toyota Honda etc. And that's before you factor in rebates...

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