1. Why are the enclave the bad guys ?
The enclave isnt bad. They are actually tring to help america but the way they want to do that is by controllling everything in the capital wasteland. But the brotherhood is trying to protect those people but the enclave thinks the brotherhood is trying to be the government so they want to kill them, So they also kill people working with the brotherhood, and some of their leaders are real jerks.
2.THEY ARE GOVERNMENT SO WHY DOES EVERYONE WANT TO GET RIDD OF THEM?
They are the last remnants of the U.S. government, so they can have access to just about every military and social organization left and the enclave are trying to bring unity back to the USA and not to mention that the brotherhood is looking for old technology to help rebuild the what? The Old world? The old world that obliterated one another? The brotherhood is constantly looking for old technology the Enclave already has.