Because noone wants to dump a ton of work into a JSON parser they can't say is standards-compliant because it also supports C-style comments?
I also find TOML to be much a cleaner syntax than either of the two, but maybe we should just give up and make a JSON-C (for Configuration, I just made this) which supports comments.
One can usually answer the question "am I going to frequently have deeply-nested tables and/or long strings for keys" in advance, and if the answer is no then TOML is practically ideal. If it proves to be wrong occasionally than JSON is a reasonable fallback, as is just coping with the verbosity of TOML.