Manufacturers who sell both directly and via retail usually offer lower prices to retailers (and usually don't disclose those prices publicly), asking the retailers to sell at a suggested price (MSRP, often same as the direct sales price). So if you buy direct the manufacturer has a notably higher profit margin.

Big retailers can often get volume pricing which allows them to keep the prices even lower (if they're willing to reduce profit margins - and yes they do need good logistics to pull this off). Typically the retailers try to make up for the lower margin in volume of sales (and/or by convincing you to buy other higher margin stuff from them too), like when an electronics store selling you an iPhone tries to sell you insurance and accessories to increase their margin since that range of phones are low margin items.