The fact that trefoil knot is knotted, i.e. not equivalent to the trivial knot, was first proved in the early 20th century by Wirtinger and Tietze. They used knot groups, though there are now countless other methods to do it, like Fox 3-colorings and the Jones polynomial.
But I think it's fair to say that humans have intuitively believed that the trefoil is knotted approximately forever. I also think it's fair to say that the intuition behind our belief is neither based on knot groups, nor Fox 3-colorings, or even the Jones polynomial. It's based on the notion that however you move a trefoil around, it's never going to become a trivial knot, a notion that is clear to anyone who plays around with a trefoil.
So my question is, is there any proof of the fact that the trefoil is knotted that captures this intuition? Perhaps a direct proof that no ambient isotopy changes the trefoil into a trivial knot, rather than a proof that resorts to knot invariants? Our does our intuition bear absolutely no relation to the actual reason why the trefoil is knotted?
I first want to express my hesitation at answering the question the way you pose it here. Intuition is extremely valuable, but it can lead you astray if you are not careful. Nonetheless, I understand that you want an intuitive proof that shows the trefoil is not the unknot.
The problem comes from the fact that there is no way, in general, to be sure we have "simplified a knot all the way." But the trefoil is an alternating knot, which is a special kind of knot. Tait conjectured:
And this was proven later by Kauffman, Murasugi, and Thisthlethwaite using the Jones polynomial. This is a highly non-trivial proof, but the thing you want is in some way contained in that conjecture. So find a three crossing diagram of the trefoil and notice it alternates and you are done!
Now, I want to point out that this is not proven for non-alternating knots, because it is not true for non-alternating knots. You can almost surely prove any individual knot you come across is non-trivial with some work, but knots can be trivial and not look that way at all. I will just reference this post on MathOverflow for some very unfriendly unknots that they have pictured there, so I will not repost them here.