Most of the time, when a manga or game is made into anime, the original creator are giving away the right for derived products to the "anime production committe" which consist of investors for production of the anime. This usually includes the publisher, anime studio, and stakeholders such as recording company and goods makers.

For example you want to produce mug with character from Ore no Imouto. You can't ask it to Kadokawa who published the novel, you have to go to the production committe who usually already have company that produce merchandises and hold the right to sell that license to foreign business.
Bakemonogatari, you'll probably have to ask Aniplex instead of Kodansha who published the novel.

Publisher are left with the right to produce printed product (the books) and to certain extent, "not for sale" promotion items.

Of course this is not the norm. If the publisher is strong, they can dominate the committe and keep the biggest power in their hand. Usually, they don't.

Author and publisher still get part of the royalty. The only have no say in deciding who can buy the merchandise license because that right has been handed over to the "production committe"