Have the add on domains all got separate hosting? or do they point to a single location? We have a reseller account so I setup separate hosting accounts for each domain and 301 to where ever from there. We mainly use windows servers though so the htaccess option isn't an option
The only thing I can think of is setup a new hosting account and move all the add ons to that?
The sites in question don't warrant reseller or separate accounts - unfortunately.... I have 6 large accounts plus a reseller with different ip's but still not worth me moving everything about (databases etc..)
You pretty much want to do the only thing that you cant do when dealing with multiple domain hosting which is all in the same hosting account.
Doh!

If you place the htaccess file in the root its going to redirect everything including the sub folders and therefore add on domains.
That's exactly what's been happening.
Oh well, I'll have to leave it as it is!
Or redirect all pages except the home/root domain page - that's doable... then put a simple html page on the homepage with a huge "Go Here" link. That's probably what I'll do.