THe Catholic News Service should have entitled this article "Catholic/Orthodox relations still a unholy mess". That seems to be the tenor of the Cardinals comments instead of Muslims really. Orthodox and Catholics still hold the wildest grudges and believe the wildest things about each other in that region.
If it weren't for the UN and NATO bowing to the Bosnian Muslims, the Catholics would be safely reunified with Croatia and the Orthodox Christians with Serbia & Montenegro.
What Mr. Puljic is hinting at is a separate Croat entity (hence "the same rights as Muslims and Serbs"). They should've thought of this and similar issues before ganging up on the Serbs in 1992.
It is up to the imperial overlords in Bosnia to allow the Croats their own province/region/whatever to come into existence and the Serbs have nothing to do with that.
The Croats were initially allies of the Bosnian Muslims and even allowed weapons and fighters for the Muslims to come through Croatia. Croatia skimmed off a significant percentage of the weapons for itself, however. For a time, when the foreign fighters (Mujahideen) and some local Muslim forces attacked Croats (approx. Oct 1992-Feb 1994), Croatia halted the "humanitarian aid" to Bosnia.
However, the U.S. State Department wanted those factions to kill and ethnically cleanse Serbs together, and brokered a deal to reunite them in late February 1994. Together again, the Muslims and Croats attacked Serbs until the end of the war.
Croats, though, are unhappy in the Muslim-Croat Federation they joined in with the Muslims. The Muslims are oppressive and have ways to create a slow, permanent ethnic cleansing by making it hard to survive, examples which were outlined in the article.
The Croats want a separate entity, like the Serbs have, to control themselves. They feel that's the only thing which could guarantee longtime survival in Bosnia.
The Muslims would be against that, as they are against the existance of the RS. They want control over all Bosnia where they would dominate. The Serbs would be in the same position as the Croats if they lose the RS, which is why they don't want the government centralized. Centralization is doom for everyone but the Muslims who do not and will not run a government fairly and respecting rights of Croats and especially Serbs.