No. Aside from meta.stackoverflow, reputation on the per-site-meta's is the same as your reputation on the parent site.
From the meta FAQ on SU which is similar to the others:
What is reputation?
You must have at least 5 reputation on
the main website to participate on
Super User Meta.
Reputation here is entirely derived
from the main website; your reputation
is the same here as it is there,
synchronized hourly. Votes here do not
affect your reputation in any way.
However, you can earn unique badges
here on the meta site.