Or they were opportunists, and used the Federalist majority to pass legislation intended to, among other things, silence anti-Federalist publications.
Ultimately, the federalists won. The last kiss of death was circa 1930s, when you see that before you needed constitutional amendments to regulate child labor (never passed) or to federally regulate intrastate alcohol (passed), after that they just totally dispensed with any of the constitutional provisions made to the anti-federalists and just rammed it all down our throats under the guise of interstate commerce.
This is why the civil rights act in the 19th century was found unconstitutional, but the mid 20th century version with many of the same provisions magically was. Or why they needed an amendment to ban alcohol, but magically did not need an amendment to pass the controlled substance act.