Correction: when they use arms.
Essentially what Adams is saying is that citizens should only use arms [against other people] for self-defense, or as directed by the government; they are not to act as non-governmental vigilantes. For citizens to use their arms in vigilante actions would be to undermine even a fully-legitimate government.
To be sure, John Adams fails to recognize what should have been additional non-governmental uses for weapons (e.g. hunting, practice). He also fails to recognize that use of arms against lawless government personnel may need to extend beyond individual self-defense (e.g. Battle of Athens, ca 1946 or so). Even he, however, did not come anywhere near implying that citizens shouldn't possess arms or be able to use them in their own defense.
Correction accepted.