Oh, I think I already found an option. It is located in the "Project" section of the doxywizard, "EXTENSION_MAPPING". Here are the options that now work for me:
FILE_PATTERNS = [...] *.ino
EXTENSION_MAPPING = ino=c
And the tag that gets me every time: A file tag must be added to the top of the file, otherwise Doxygen is ignored. For instance:
source
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