Just a couple of points:

1) Eric, I imagine that I’m
missing something (no jokes, please), but in Madison’s quote that you
cited, where does he mention the Constitution itself for support of the
country’s principles?

2) John, I think Hamilton was serious–expressly stating
some rights can cause a problem because other rights may not get
protected.  This type of legal analysis is valid (and is done all
the time).  If a legislature passes a bill that says Citizens A
has X rights, but doesn’t mention Y rights, then it is reasonable to
argue that the legislature didn’t intend to make Y a right.  To
read Y into the law probably is an act of judicial activism (not all of
the time).

The bill of attainder point is valid but it is not “packaged”
within a list of rights, nor do I think it can be called a right–it is
a restraint on Congress.  I know the Bill of Rights limit
governmental power too, but they are expressly listed as rights and do
not appear in Article I.