Yes, there are real paid shills deployed by government funded groups like Media Matters. No, not everyone who disagrees with you is a shill, but they DO exist. Anything detrimental to the establishment, they will shill on. Be skeptical.
A shill, also called a plant or a stooge, is a person who publicly helps or gives credibility to a person or organization without disclosing that they have a close relationship with the person or organization.