The ale for breakfast or ale in place of water was not beer as we know it today. It was a "small beer" of very modest alcohol (less than 3% abv) brewed specifically to be more nourishing and less intoxicating than today's common beverage. Naturally the brewing process makes it safer to drink than untreated water. The alcohol also has a preservative effect but the thick, sweet, unattenuated ale is also a good source of calories. Sure, some of that barley could have been eaten in whole form instead of being processed but not all nutrition is lost. Yeast is healthy and I don't think there is really anything dangerous capable of living in beer than is dangerous to consume, though it may not taste good. I don't know this for a fact but this is what I learned while getting into homebrew about 10 years ago. I have not brewed anything for 5 years or more. I do suspect that shorter life expectancy in historical times negated the prolonged effects of alcohol abuse that we are now familiar with. The increase in cost and rarity probably made heavy consumption more inconvenient, to say nothing of modern serving sizes. I wasn't alive to see it but I have trouble believing some modern notions that entire populations would have been drunk all day, every day, for centuries on end. It's just alcohol. A little bit taken a few times a day does not necessarily make you inebriated, unhealthy, or less productive. Ounce for ounce in your average beer variety I find alcohol to be just as stimulating (the perceived affect) both mentally and physically as coffee. Your mileage may vary. I feel quite gifted in this regard
FWIW I have heard the tradition of kvass, a related type of bready low alcohol nourishment, is still common in Russia. I also drink far, far greater quantities of caffeine than alcohol.