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Is it safe to soak dry beans overnight at room temperature before cooking?

Yes, it is safe but there still is some risk for foodborne disease so it is recommended to not follow this practice. If vegetative pathogenic bacteria are present, they could grow to harmful levels. However, the high temperatures required to cook the beans alone or as part of any menu item would be sufficient to kill them.

To be safe, it is best to use the quick soak method -- bring water and beans to a boil, cover, and boil for two minutes. Remove from heat and let stand one hour. Drain and further cook. If this is not possible, then soak the beans in the refrigerator overnight.