I'd agree that with these sort of regional/captive carriers they are generally tied completely into the FF program of the "parent". However, don't assume they are all subsidiaries:

Jazz - independent, publicly traded; but substantially all capacity is purchased through a Capacity Purchase Agreement with Air Canada. Jazz is slowly branching out into direct charters.

Comair - wholly owned subsidiary of Delta.

American Eagle - a "system" of AA, consisting of American Eagles Airlines Inc., and Executive Airlines Inc., both effectively owned by AMR.

Swiss European - wholly owned subsidiary of Swiss.

Other carriers have both subsidiary and independent companies flying under the same regional brand for them, but as far as I know, that makes no different to FF program.