Your interpretation makes no sense in a few different ways. First: The Federalist Papers are arguing in support of the core Constitution at a time before the Bill of Rights or 2nd Amendment existed or had even been proposed. Second: Once again, the argument by Hamilton is not that random ownership of guns will protect liberty, but actually the exact opposite. Federalist No. 29 is specifically in support of the the fact that the Federal government needs to be in charge of an elite armed forces, and that this is "the best possible security", that the people as a whole cannot possibly be up to the task. The only question here is whether this well-trained and Federally-organized "select corps" is a full-time army or a part-time militia. Here's your quote in context of the full paragraph:
"But though the scheme of disciplining the whole nation must be abandoned as mischievous or impracticable; yet it is a matter of the utmost importance that a well-digested plan should, as soon as possible, be adopted for the proper establishment of the militia. The attention of the government ought particularly to be directed to the formation of a select corps of moderate extent, upon such principles as will really fit them for service in case of need. By thus circumscribing the plan, it will be possible to have an excellent body of well-trained militia, ready to take the field whenever the defense of the State shall require it. This will not only lessen the call for military establishments, but if circumstances should at any time oblige the government to form an army of any magnitude that army can never be formidable to the liberties of the people while there is a large body of citizens, little, if at all, inferior to them in discipline and the use of arms, who stand ready to defend their own rights and those of their fellow-citizens. This appears to me the only substitute that can be devised for a standing army, and the best possible security against it, if it should exist."
I recommend that anyone read the whole paper, it's pretty short and highly illuminating to the true purpose of a Federally-run armed force, specifically in contrast to disorganized and undisciplined random mobs.
http://www.foundingfathers.info/federalistpapers/fed29.htm