It may have to do with the fact that while the antibiotic is circulating, your immune system is not currently reacting to the bacteria's sudden presence, so it doesn't bring the antibiotic into play. Your immune system doesn't go after anything until it recognizes a danger, which it does in a series of complex, chemical events.
If no bacterium finds a toehold in your heart or valves, the massive upwelling of immune responses never really occurs, and macrophages and other cleanup cells (phagocytes) in your blood simply encounter, engulf, and carry most of the bacteria harmlessly away.
The antibiotic bolus probably leaves your body long before the immune system could pick up any colonization or danger signals. Even bacteria take some time to multiply.
In the end, though, the apparent logic of prophylactic antibiotic use isn't what matters. The cold science is that, reasonable or not, it simply does not work. (No, not even a little.)
It's hard to look at a situation in which you've always been told you were protected (by people you were taught to trust), and find that you were actually riding into the battle naked and alone all this time. You want the feeling of protection and confidence you used to have back again.
Something like trusting a financial advisor with your retirement investments, and finding out that now you've not only not made any of the profits he always assured you of, but you've actually lost some of the original money you invested, and your house investment isn't worth anything anymore either. (This is just to illustrate the point: this type of upset happens in all kinds of professional fields, with all manner of trusted "experts.")
Moral: Don't rely solely on experts. If something important to you doesn't make sense to you, shake the truth out for yourself.
Best wishes,