No, bacterial size does NOT matter for infectivity. Though it is true that the largest cells (a common egg cell) is eaten as food. Normally you body just digests any bacteria pretty much the same way. The really tiny viruses are typically debated as being truly "living". They are mostly just bundles of DNA and attack bacteria. Again, your body will simply digest them.
Unless you have highly expensive filters, most are simply statistically designed. They lay out layers pretty much randomly. Soo, typically, they design a .1 micron filter, and sell it as a .2 micron filter, knowing it will catch most things at .2.
A scientific filter may cost hundreds of dollars. These are absolute and will NOT pass anyhing other than 1 micron. That said, I would not worry to much. Your body has been dealing with that stuff throughout evolution. Most stuff might make you "scoot". If you are immune compromised, boil the water.
Viruses and bacteria in the water can be bad. And yes. In the US as well as the rest of the planet, you may find some, as Roger says. The big difference in the US is that if you were born in the USA, then you probably were immunized against the worst of these. Polio, smallpox, hepatitus, and a host of others. You are likly immune to them and can ignore these. NOT from fecal mater, bead and decaying tissue, etc, though. Use normal caution, use ALL your senses: taste, looks, smell and feel.
I have drunk from lakes in the ADK's for many years. Then I heard that the upper layers were pretty clean due to UV. Soo, I cannot say whether this is true or not, since the lack of evidence says nothing. But, I would not recommend trying this near shore. The wave action churns up too much crap in the water. In a canoe, I would not object, though.
I treat mainly for bacteria and viruses. Crypto, Gardia, I pretty much ignore. If I have a case of the "scoots", it will likely NOT be out camping. It takes a week to a month to develope.
Tapeworms are another concern. UV is not that effective on macrobiotics. Filtering is good. Boiling always works.