This can get pretty confusing sometimes. Most, if not all skeins of yarn have a small chart on the tag letting you know the size hook you should use with that particular yarn, but that doesn't mean you can't break those rules. I do it all the time.
Sometimes you will want tighter stitches without having to kill your hands to get them, go down a hook size, however, I don't recommend doing this with a crochet thread. Crochet thread is already torture on a spool, don't make it worse on yourself! Just remember this will change the size of your finished piece, weather it's a scarf or an amigurumi.
The same can be said for wanting looser stitches, go up a size with your hook. I don't recommend doing this with an amigurumi, you want those stitches as tight as you can get them so you can't see the stuffing..
All the information I state here is mostly for amigurumi, If you're making a shirt and the pattern says to use a specific size yarn and hook, do it. You're finished piece will be smaller or larger than you want it to be if you don't.
There are no hard and fast rules when it come to crochet, no one will ever convince me otherwise, yes there are ways you have to make the stitches and you have to use a hook, but when it comes to brand of yarn or the size you want something. Do whatever the heck you want. It's your piece, you have to be happy with the outcome.