Yeasts are naturally occurring in the environment. It is like any bacteria or mould. Think about your fridge and how food goes mouldy or "off". It is because a microorganism in the environment surrounding the area has been there long enough to grow and colonise.
Wild yeast is the same, it is a naturally occurring living organism. I have had bakery teachers talk about making bread with fermenting wine, sort of like a sourdough, so the natural yeast in wine will also grow from the carbohydrate in the flour. Basically, if you wanted to make wine or beer, you could just leave any liquid containing microorganism "food" eg a sugar or other type of carbohydrate out and eventually it would go off and begin to ferment. Of course this is not safe to drink until enough alcohol has been created and the alcohol content is enough to kill off the living micro organisms. Bread technically could be made from wild yeast in the air, however, it is most likely that families had a growing "yeast" that they kept in their households. They would take a small amount, and add it to that day's bread, and leave the rest for the next day. Once you isolate that yeast, it will grow and grow and grow, so every time you take a bit away, it will re-grow. Families or communities would have had their own special supply.
This type of inoculation is still how some people make things today. You can make your own yoghurt for example by boiling fresh milk (brining the bacteria count back or near to zero) and once cooled, adding a spoonful of yoghurt. The bacteria present in the spoonful of older yoghurt will grow and spread throughout the milk and turn it in to yoghurt. This can sometimes be dangerous and in today's world, is generally not a commercially acceptable process as you could mistakenly introduce a harmful yeast or bacteria into the food instead of the particular strain you want.
It is more than probable that flowers or hops, as you mentioned, contained this wild yeast and were able to ferment the bread and help it rise.
Long story short: Everything we touch has naturally present microorganisms. So the same way you could catch the flu or get an infection, is also the same way they were able to make wine and breads and yoghurts and cheeses.
:)
Mostly they used "Starter Dough" or "mother dough" A single batch of leavened bread that had naturally acquired the right yeast would be split. You would add flour and water to the starter dough and after it rose you would bake some and leave some for starting the next days bread. Early bakeries would sometimes jealously guard their mother dough.
Boudin Bakery in San Francisco has been using the same batch of sourdough "Mother Dough" since 1849.
Wild sourdough is still commonly made - I have a wild sourdough culture I use every weekend to bake bread. If you want more details or directions, I can provide them.
First of all, not every bread have yeast. First breads were just made from water and flour and some still are (like Jewish matzo).
Later bread was (and still in many countries is) made from sourdough. It needs more work and longer rising, but it's superior in taste (ok, this part is my personal opinion).