Stores like to do so as they gain good will and can advertise that they helped charities out. Charities get free advertising and extra donations. The store does not gain monetarily* from the donation: at best, they would need to claim both the income and deduction for no change in taxes, however they practically will always handle it as a passthrough donation where they claim neither.
The store should have the information available to allow you to deduct the donation yourself, though you may need to specifically request it. Given the current standard deduction in the US, very few people are likely to donate enough for it to matter, however.
Many of the stores have a charity under a very similar name as the store’s name that will be the typical recipient of the donations. For example, McDonalds has the Ronald McDonald House Charities and Albertsons/Safeway/Vons (are three are owned by Albertsons) has the Albertsons Companies Foundation.
* The store is allowed to take a small amount of processing fees for the transaction, which may be in the range of 1-7%. These fees will typically be similar to what would be taken if you make a donation online.
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