Of works but has (to me) a hint of that you couldn't be bothered to find a more specific word.
From is best, and only weakly implies an exhaustive list. "Beer is made from (among other ingredients) malt and hops" is perfectly sensible with or without brackets. Especially as water is a rather obvious ingredient.
With is just too vague - it could even be taken to mean "in the same factory as", e.g. "beer is made with cider in a brewery" (UK meaning of cider).
Out of has the flaws of of but a stronger suggestion of exclusivity.
Strictly speaking beer is brewed from malted barley and water, using yeast, and only flavoured with hops, however it would seem sensible to ignore this distinction as the hops are fundamental to beer. The yeast is not an ingredient in the cooking sense - it takes an active part in the process.