For me, the way I think about rotations is a consequence of the maximal torus theorem for $\mathrm{SO}(n)$. Namely, given any $A\in \mathrm{SO}(n)$ (i.e., a rotation of $\mathbb{R}^n$ which fixes $0$), there is some basis of $\mathbb{R}^n$ with the property that in this basis, $A$ consists of a bunch of regular $2$-dimensional rotation blocks.
More precisely, writing $R(\theta) = \begin{bmatrix} \cos\theta & -\sin\theta \\ \sin\theta & \cos\theta\end{bmatrix}$ for the standard counterclockwise rotation matrix, there is always an orthonormal basis of $\mathbb{R}^n$ in which $A$ takes the block diagonal form $$A=\begin{cases} \operatorname{diag}\Big(R(\theta_1), R(\theta_2),..., R(\theta_{n/2})\Big) & n \text{ even}\\ \operatorname{diag}\Big(R(\theta_1), R(\theta_2),..., R(\theta_{(n-1)/2},1)\Big) & n \text{ odd}\end{cases}.$$
This indicates that rotations are fundamentally two-dimensional ideas which are then bootstrapped to higher dimensions. In fact, it gives a recipe for constructing all rotations of $\mathbb{R}^n$: Pick any $2$-plane and rotate it a bit. In the orthogonal complement, pick any $2$-plane and rotate it. In the orthogonal complement of these two $2$-planes, pick any $2$-plane and rotate it, etc.
Thinking about $\mathbb{R}^3$ for a moment, a rotation in the $xy$-plane doesn't change the distance from a point in the $xy$ plane to any point in the $z$-axis. In fact, a rotation in the $xy$ plane has no effect on the $z$ axis. The above decomposition indicates that this idea propagates to higher dimensions. For example, in $\mathbb{R}^4$ (with coordinates, say, $(x,y,z,t)$) a rotation in the $xy$ plane doesn't change the distance from a point in the $xy$ plane to a point in the $zt$ plane.
This is why, for example, your action on $\Bbb S^3$ can rotate two things in opposite directions. It's hard to visualize, but a rotation in the $xy$-plane has no effect on the $zt$-plane, so no "twisting" of $\Bbb S^3$ occurs in your action.
On the other hand, for your cylinder action, note that your action is not a rotation of $\mathbb{R}^3$ restricted to the cylinder, so none of the above applies. In fact, I wouldn't call your action on the cylinder a rotation. It is a rotation on each boundary component, but who knows what it is in between!