After the toilet flushes and fills up
Then shuts off
The pipes under the house start shaking rattling, hammering
Why
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This is called "water hammer" and is caused by water slamming into elbos. Your air chambers need recharging. Let me show you how. Back in the 60's we were required to to put shock absorbers,(air chambers) on all bath lavatorys and kitchen sinks. Over time water and condensate built up in them and they must be recharged. First turn off the house at the main house shut off valve. Then open hot and cold faucets at the farthest bathroom to prevent air lock.(This is important.) You will find under each fixture little brass or chrome valves. These are called angle stops. With a small pail held under the angle stop to catch the run off look under the handle of the stop and you will see a nut with the stem running through it. This is called the bonnet packing nut. Put your wrench on it and back it off counterclockwise. Now open the stop and remove the stem and washer assembly, The stop will begain to drain. When it has quit draining reassemble the stop and move on to the next one. Do this on each one of your angle stops. There will be six of them in a two bath home. When you are done, close off the faucets you have opened, turn on the water to the house, and give yourself a pat on the back.
You have just recharged your air chambers and saved yourself a hefty service call bill.

This could also be "seat chatter" in the toilet ballcock, but since it affects pipes under the house and not the toilet tank I would check and recharge your air chambers. Good luck, Tom

Tom is 100% correct if this is just one hammer noise. If it is a rattle or several hammers I think your valve is fluttering and not shuting down completely. If you can't figure how to open the ballcock and inspect the seat just install an entirely new ballcock but don't buy the cheapest one on the shelf. I still like good old brass ones.