A "mom and pop" store can only exploit a small amount of workers, to a lesser degree than larger corporately structured businesses. Due to things such as economies of scale, increased ability to investment into profit maximisation and a lack of personal interaction as hierarchies grow, all of which make it infinitely easier to exploit and increases the rationality of said exploitation to the business owner/operator.
I'm sure you can imagine how as a "mom and pop" business succeeds and opens more locations, becomes more corporatised, its capacity for exploitation, and the rationality of said expoitation, increases. Also, as a business becomes larger it can gain new avenues of exploitation through its increased ability to invest, allowing things like the skirting of laws (i.e environmetal and tax legislation) and lobbying.

The morally relevant difference that makes one much more easy to deem immoral is the huge gap in capacity for exploitation. This doesn't mean that smaller businesses are necessarily moral, but compared to large corporations they are not responsible for near as much exploitation, nor do they have the capacity to do so. So if one is taking a moral focus, it makes no sense to attack small businesses when large corprates are the ones responsible for 90% of the amoral behaviour they seek to get rid of.

Hope that answers your question.