In flymake-mode.el is the following commented-out line:
;;+(add-hook 'find-file-hook 'flymake-find-file-hook)
It has not been touched since 2005, and the commit log then suggests it
was merely moved from another place; I can't find any other reference to
it in the bzr logs.
According to the manual, adding this hook to find-file-hook is the
recommended way to activate flymake-mode automatically, and that is
never done. Nor can I find a way to turn flymake-mode on automatically
with customize; it seems the best I can do is copy the above line,
uncommented, into my Emacs initialization file.
It is far from obvious that the line above should be uncommented, but if
not, maybe it should be removed, and a more user-friendly and standard
way of activating flymake-mode automatically added?