Thanks for writing. Squirrels --- like people --- have different tastes. Just like one person may really enjoy sauerkraut and another person may hate it, one squirrel may may enjoy marigolds even though the majority of them don't.
You can try spraying your marigolds with a product called Hot Pepper Wax; look for it at your local garden center. Also: If they didn't eat the marigolds to the ground, the plants will probably come back. The squirrels may leave them alone --- sometimes they cause damage because they're curious about a newly planted flower. Once it's in the ground for a while, they typically lose interest in it.
---Justin, Senior Garden Editor, BHG.com