How to get all the instances of a custom entity via Web API?

Use the /api/<entity name> request.
You can find out an entity’s name using the /api/doc/rest_json_api request.

An example

curl -i -k \
	-H "Accept: application/json" \
	-H 'Authorization: WSSE profile="UsernameToken"' \
	-H 'X-WSSE: UsernameToken Username="Dmitry Fedyuk", PasswordDigest="ya9BoQFPMgrV66x7aW+F937qKE0=", Nonce="NmVkOGMzN2VjZjE5MTllOA==", Created="2017-06-03T23:50:42+03:00"' \
	https://localhost.com:848/app_dev.php/api/extenddfcustomers