If you have two statements P and Q, and we say that P implies Q, that suggests that P contains Q. So if we have P, we must have Q because it is contained within P. This is my intuitive understanding of the implication.
On the other hand, if we do not have Q, by my example above it would not imply that we do not have P, since Q is only one of the things contained within P. So why would showing that when we don't have Q we don't have P prove the implication?
In short, what understanding of the material implication is needed for proof by contrapositive to make intuitive sense? I understand the truth tables are the same, but that does not provide intuition in my opinion.
Since it seems you are thinking in terms of subsets, It is like saying that if $P\supseteq Q$ then $Q^c\supseteq P^c$ (in the sense that if $P$ is the set of all things we know to be true as our hypothesis, then the entirety of $Q$ is among those things we know as a result to be true. On the other hand if $Q^c$ is the set of all things we know to be true, then the entirety of $P^c$ is among the things we know to be true)
In the following image, $P$ contains $Q$ as a subset. The lighter shade indicates that it is used by both $P$ and $Q$.
On the other hand, looking at the complements, the area outside of $Q$ (part, not all, of which is red) contains the area outside of $P$ (in pink) as a subset. Again, the lighter shade is the area used in both.