For the Fourier transform there are primarily two issue:
1. The "complex plane" - this tries to make complex numbers somehow less scary and more intuitive? But it's actually a useless crutch that gives people a false sense of understanding. The core issue is that you can multiply two complex numbers and get another complex number. If I give you two vectors or two points on a map and tell you to multiply them.. you can't - b/c that is not a defined operation. We have no intuition about how to multiple 2D numbers (you might think, oh dot products and cross products! but those are something unfortunately unrelated)
2. "Frequency Space" and an the constant suggestion that your signal is somehow being broken up into it's magical innate hidden frequencies. This is also very deceptive (or doesn't hold up in the discrete case). The basis is selected to be mathematically convenient (ie. orthogonal) and is based on your sampling window and properties of complex numbers. These may correspond to some underlying natural frequency that's occurring - or it may not. But it's not helpful to try to confound the two
If you instead approach the whole problem from a purely mathematical perspective of projection on an orthogonal basis and how to construct complex values that are convenient - then the whole setup is less "fun" but it actually becomes a lot more understandable. You can then move on from there and start asking yourself much more interesting questions about aliasing, ringing, fm/am, phase etc.
I feel it took be ~5 attempts of learning Fourier Analysis to unwire my brain and unlearn these bad visual intuitions that send you down the wrong path