Per se lower quality? No.
There are lines which produce very cheap motherboards. I suspect (-with no hard evidence to back that up!-) that most use cheaper components.
However things get quite muddled at the cheaper end. E.g. consider the Cyrix 200+ CPU. Sold very cheap compared to the pentium-1. Often found in desktops with the cheapest possible power supplies, the cheapest possible motherboards, the cheapest possible graphics cards... and often in an unstable system.
Unsurprisingly it had a very bad name, yet one ran without problems for years in an old Asus boards with good hardware.
The point of that anecdote is to point out that a piece of cheap hardware can be worse quality, but it does not have to be. And that mouth to mouth experience in this case is often wrong.
Having said that: Your motherboard is the backplane of all other components. Both on add-in cards or integrated. Getting a good motherboard is worth it. So do read reviews of which board you are considering, but do so with a critical eye.