That's not necessarily true. Boiling will protect you from ingesting live parasites or bacteria, but it will not protect you from potential toxins that might have been produced by the bacteria. It will not protect you from pollutions like heavy metals either, but neither will alcohol.
Alcohol would have the advantage over boiling water that the bacteria would not be in the alcohol in the first place so they could not have produced something bad for you in the water. Also, as someone else pointed out, if you don't understand why some water makes you sick, and don't understand how to treat the water to keep it safe, how are you gonna start boiling water? Does it give you something beneficial apart from the not yet made connection of safety? no.
What gives alcohol the big advantage here is that the safety-thing is a side-effect. People drank because they liked it, and the hypothesis is they also gained better survival because it happened to have antiseptic features as well.