It makes sense within the context of the movie -- being that "the Matrix" is a "simulation".
I've read Thich Nhat Hanh describe "inter-being" as follows:
Suppose I hold a leaf in my hand. What do you see?
A leaf is a leaf; it is not a flower. But in fact, when we look
deeply in to the leaf, we can see many things. We can see
the plant, we can see the sunshine, we can see the clouds,
we can see the earth. When we utter the word “leaf”, we
have to be aware that a leaf is made of non-leaf elements.
If we remove the non-leaf elements, such as the sunshine,
the clouds, and the soil, there will be no leaf left. So it is
with our bodies and ourselves. We’re not the same as, nor
are we separate from, other beings. We’re connected to
everything, and everything is alive.
I think that's one of the aspects of emptiness ("If we remove the non-leaf elements there will be no leaf left").
I think that Zen is a bit ambivalent on the subject:
At the first level on the path he saw mountains as mountains and rivers as rivers.
On the second level of the path he saw that mountains are not mountains and rivers are not rivers.
And at a third level he saw once again mountains were mountains and rivers were rivers.
I think of it as a partial truth; possibly extremist (i.e. one side not the other, not the middle way); possibly dangerous, useful to justify immorality (e.g. "it doesn't matter if you kill people because they don't exist anyway"); possibly conceptual proliferation, letting intellectual theories run away without regard to fact. But partially true.
I think some of the facts of the matter are ably explained by the Zen story, Nothing Exists:
Yamaoka Tesshu, as a young student of Zen, visited one master after another. He called upon Dokuon of Shokoku.
Desiring to show his attainment, he said: “The mind, Buddha, and sentient beings, after all, do not exist. The true nature of phenomena is emptiness. There is no realization, no delusion, no sage, no mediocrity. There is no giving and nothing to be received.”
Dokuon, who was smoking quietly, said nothing. Suddenly he whacked Yamaoka with his bamboo pipe. This made the youth quite angry.
“If nothing exists,” inquired Dokuon, “where did this anger come from?”
The meaning of the phrase -- the way in which it may be meaningful or useful outside the movie -- might be illustrated by Persig's old South Indian Monkey Trap ...
... the most
striking example of value rigidity I can think of is the old South Indian
Monkey Trap, which depends on value rigidity for its effectiveness. The trap
consists of a hollowed-out coconut chained to a stake. The coconut has
some rice inside which can be grabbed through a small hole. The hole is big
enough so that the monkey's hand can go in, but too small for his fist with
rice in it to come out. The monkey reaches in and is suddenly trapped...by
nothing more than his own value rigidity. He can't revalue the rice. He
cannot see that freedom without rice is more valuable than capture with it.
The villagers are coming to get him and take him away. They're coming
closer -- closer! -- now! What general advice...not specific advice...but what
general advice would you give the poor monkey in circumstances like this?
... i.e. "there is no trap".
One other thing from the movie, as Neo gains in ability they say of him, "He's starting to believe." Focus on non-existence (e.g. of impediments) can be helpful I guess, another aspect of Buddhism that perhaps isn't so famous in popular culture is a focus on developing factors of enlightenment.