We use the expression
be made from when we can no longer identiy the material that was used just by looking at the object.
e.g. Almost all paper is made from wood pulp.
When you look at a piece of paper, there is no way to tell that it started out as wood pulp.
We use the expression be made out of when we can identify the material that was used just by looking at the object.
e.g. That old dresser is made out of knotty pine.
When you look at that dresser, you can tell immediately (by the look, grain and color) what kind of wood was used - if you are familiar with different kinds of wood, of course. [made of is an alternate form].
We use the expression made with when we mention onoe or more ingredients.
e.g. This paint is made with latex.