It might also help to think of the sets as being boxes, which might contain any number of objects (including infinite). For instance, the set $S = \{\text{apple}, \text{ball}, \text{corkscrew}\}$ might be represented by an actual box containing an apple, a ball, and a corkscrew.
In this analogy, the empty set $A = \varnothing$ is just an empty box. Being the empty set, it is a subset of any other set. That would mean that every item in the empty box is also in every other box. That is manifestly true: There are no items in the empty box that aren't also in every other box.
Note that the empty set is not an element of every other set. For example, the box representing the set $S$ contains three ordinary objects, but does not contain an empty box.
However, something that would contain an empty box would be $B = \{\varnothing\}$, which would be represented by a box that contains only an empty box (which would represent $A$). And $C = \{\{\varnothing\}\}$ would be—you guessed it—a box, which contains only a box, which in turn contains only an empty box.
Observe that these various boxes are evidently not the same: Something that contains only an empty box is not the same thing as an empty box.
(Please don't ask me about $\{\text{box}\}$.)