Depending on what store is asking for donations, the charity might be run by friends and family of the executives or board of directors of that store.

The charity will then spend an awful lot on compensation to the people running it. The absolute worst offender in the space was Susan G Koman. (since fixed)

The point being, there are some charities that are better than others, it’s often best to donate to them directly instead of going through a third party.