As stated above, the single biggest difference is price. That’s the effect of (usually) higher labor rates at a dealer, as well as their insistence on using only OEM parts, whereas independent shops will use universal parts that do the same job without the same cost. You also would go to a dealer for warranty or recall-related work.
I’d suggest that an good independent is the way to go for most things, as the price difference on some things can be substantial.