In short, you build your immune system up with probiotics and antioxidants. Here's a more detailed description of how your body does this for you, given a chance:

Immunity to Enterotoxigenic Escherichia coli

"Seventeen students and other community volunteers were given 106 or 108 organisms of E. coli B7A (O148:H28), which produces heat-labile and heat-stable enterotoxins. Ten individuals developed diarrheal illness closely resembling natural travelers diarrhea; of these ten, rises in titer of serum antitoxin and anti-O antibody occurred in eight (80%).

Eight of the volunteers who developed diarrhea in the first test agreed to undergo rechallenge 9 weeks later with 108 B7A organisms. Only one of these eight “veterans” developed diarrhea versus seven of twelve controls given the same challenge (P = 0.05)."

The mechanism by which Cryptosporidium causes diarrhea is still poorly understood, and so is the immune system's response to it, but for certain the risks of exposure is much higher for municipal water supplies than clear running streams in a wilderness area. It's also certain that your body can fight off small exposures if your immune system is strong. It's very unlikely you'll be overexposed when drinking from a clear running stream. Still water (a pond or pool) would increase that risk a lot if the cyst were present (and as you said, there is no fast and easy test for them).

I already pointed out that for Giardia human to human exposure is (by far) the most common way to get sick from it. The next most common is from dirt.

All this is not to diminish the need to know when you should treat your water, or knowing to err on the side of caution if you don't. It is to focus on the need to know how to evaluate a water source and to try and put the risks into perspective.

The facts are that we are most likely to get Giardia from our friends and after that the dirt we're walking on, and we're most likely to get Cryptosporidium from our kitchen faucet, and we're most afraid of getting them from water in the wilderness.

I understand the first three, it's that last one that trips me up.