Yes, brand name is a part of the price. Honeywell has been making these things for YEARS so their name is part of the price.
As for differences, I can't say if a not-so-popular brand's product is 'inferior' to a brand-name product. You have to suspect that the quality of the material is part of the price too. And so are the features of the unit.
My unit, for example, is a Honelywell 1 Zone unit. It has 4 Weeday Settings and 2 Weekend settings. It has a clock and a battery backup too. I like these features especially the battery backup. Our power goes out enough in bad weather that I don't want to have to re-program the unit every time that happens!
Shop brand, features, and ask questions. If you can find a HVAC contractor or if a friend knows one, perhaps you can ctc him about this. If you have a particular brand, make, and model, I have a contact to ask him about it. If you're interested in a few different ones, get me the info and I'll see what I can do.