Equations of Motion
What you are describing is Hamiltonian's view of the evolution of a
dynamical system. $\mathbf q$ is the vector describing system's configuration with generalized coordinates (or degrees of freedom) in some abstract configuration space isomorphic to $\mathbb R^{s}$. For instance $s=3n$ particle coordinates for a system of $n$ free particles in Euclidean space. $\mathbf p$ is the vector of generalized momentum attached to instanteanous time rate of the configuration vector. For example for particles of mass $m$ in non-relavistic mechanics $\mathbf p= m \frac{d}{dt}\mathbf q$. Classical mechanics postulates that the simulteanous knowledge of both $\mathbf q(t)$ and $\mathbf p(t)$ at time $t$ is required to predict the system's temporal evolution for any time $t'>t$ (causality). So the complete dynamical state of the system is in fact described by the phase $\mathbf y =(\mathbf p, \mathbf q)$ which evolves in an abstract space called the phase space isomorphic to $\mathbb R^{2s}$. The fact that the knowledge of this phase is sufficient to predict the evolution demands on a mathematical point of view configuration $\mathbf q$ to evolve according to a system of $s$ ODEs of at most second order in time (known as Lagrange equations) or equivalently that phase evolves according to a system of $2s$ ODEs of the first order in time knwown as Hamilton's equations of motion,
$\frac{d\mathbf p}{dt}=-\frac{\partial H}{\partial \mathbf q}(\mathbf y,t)$
$\frac{d\mathbf q}{dt}=\frac{\partial H}{\partial \mathbf p}(\mathbf y,t)$
given some Hamilton's function $H(\mathbf y,t)$ describing the system. Physically it represents mechanical energy. For non-dissipative systems it does not depend over time explicitely. as a consequence of Liouville's theorem it is a conserved quantity along phase-space curves.
More generally, equations of motions appear to be formulated as a system of Euler-Cauchy's ODEs
$\frac{d\mathbf y}{dt} = \mathbf f(\mathbf y,t)$
\with $\mathbf f$ some vector-function over $\mathbb R^{2s}\times\mathbb R$
In accordance with Hamiltonian formalism, $\mathbf f$ appears to be
$\mathbf f= (-\frac{\partial H}{\partial \mathbf q}, \frac{\partial H}{\partial \mathbf p}) $
Liouville's theorem
Now consider the phase flow $\mathbf y_t$, that is consider the one-parameter ($t\in \mathbb R$) group of transformations $\mathbf y_0\mapsto \mathbf y_t(\mathbf y_0)$ mapping initial phase at time $t=0$ to current one
in phase space. This is another parametrization of the phase using
$y_0$ as curvilinear coordinates. Suppose you have now hypothetical
system replica with initial phase points distributed to fill some volume $\mathcal V_0$ in phase space. Liouville's theorem says that the cloud of points will evolve such as preserving its density along their curves
in phase space, like an incompressible fluid flow, keeping the
filled volume unchanged. Since
$\mathcal V(t)=\int_{\mathcal V_0} \det \frac{\partial \mathbf y}{\partial \mathbf y_0}(\mathbf y_0,t)\ \underline{dy_0} = \int_{\mathcal V_0} J(\mathbf y_0,t)\ \underline{dy_0}$
Now compute the volume-change time rate at any instant $t$ introducing Euler's
form (1),
$\frac{d\mathcal V}{dt}=\int_{\mathcal V} \frac{\partial \mathbf f}{\partial t}+ \nabla_{\mathbf y_0} .\mathbf f(\mathbf y_0,t)\ \underline{dy_0}$. Setting this time rate to zero gives Liouville's theorem in local form:
$\frac{\partial \mathbf f}{\partial t}+ \nabla_{\mathbf y_0} .\mathbf f(\mathbf y_0,t)=0$.
Applying them to Hamilton's form,
$\frac{\partial }{\partial t}[\frac{\partial H}{\partial \mathbf p}-\frac{\partial H}{\partial \mathbf q}] + \frac{\partial}{\partial \mathbf q}\frac{\partial H}{\partial \mathbf p} - \frac{\partial}{\partial \mathbf p}\frac{\partial H}{\partial \mathbf q}=0$ (1)
For conservative systems in energy, $H(\mathbf y,t)$ does not depend upon time explicitely and the left-most term in (1) vanishes. Liouville's theorem can be generalized to any physical observable depending upon the phase of the system $A(\mathbf y,t)$ which is a conserved along the curves of the phase space,
$\frac{dA}{dt}= \frac{\partial A}{\partial t} + \frac{\partial A}{\partial \mathbf q}\frac{\partial H}{\partial \mathbf p} - \frac{\partial A}{\partial \mathbf p}\frac{\partial H}{\partial \mathbf q}=0$
The Wronskian
Now consider the situation of Euler's ODE can be linearized around phase
$\mathbf y_0$. The vectorial function $\mathbf f$ now expresses as a matrix
vector product with the phase. You have now a $2s\times 2s$ square
linear system of ODEs.
$\frac{d\mathbf y}{dt} = {\mathbf f}(\mathbf y_0,0)+M_{\mathbf y_0}(t)(\mathbf y-\mathbf y_0)+\ldots$
with $M=\frac{\partial f}{\partial \mathbf y_0}$.
One can solve a new system of the form, $\mathbf y'=M_{\mathbf y_0}(t) \mathbf y$ for any translated phase around $\mathbf y_0$.
Consider $2s$ phase solutions of this system $(\mathbf y^1, \mathbf y^2,\ldots, \mathbf y^{2s})$. Then the wronskian
$W=\det(\mathbf y^1, \mathbf y^2,\ldots, \mathbf y^{2s})$ satisfies
the first-order ODE,
$\frac{d}{dt}W= \mathrm{tr}(M_{y_0}) W$
and can be integrated as
$W(t) = W_0\exp \int _0^t\mathrm{tr}(M_{\mathbf y_0}(s)) ds$
Hope this helps.
There are two ways to read your question since you use the phrase "Hamiltonian isotopy", rather than the related notion of "Hamiltonian symplectomorphism"-i.e. a symplectomorphism which Hamiltonian isotopic to the identity.
V1. Is a symplectic isotopy a Hamiltonian isotopy?
No, see Proposition 9.19 of "Introduction to symplectic topology" (Second edition).
V2. Is a symplectomorphism which is isotopic (or even symplectically isotopic) to the identity a Hamiltonian symplectomorphism?
The answer is also no. See see the symplectomorphism of $T^*{S^{1}} $constructed here: Showing that some symplectomorphism isn't Hamiltonian. It is symplectically isotopic to the identity by $F_{t}(x,\xi) = (x,\xi + t)$, but it is not a Hamiltonian symplectomorphism as is proven there.
Best Answer
This is not a Hamiltonian symplectomorphism.
First, once $S^1$ is a Lie group, its cotangent bundle is a product and, in fact, can be thought as a cylinder. So the transformation in question is a translation of this cylinder $C$. If we wad a Hamiltonian
$$H:C\rightarrow\mathbb{R}$$
then its gradient will be orthogonal to the symplectic gradient. The symplectic gradient must be the field wich will give rise to the isotopy. But the gradient field of $H$ should be everywhere-non zero and tangent to $S^1$, which is impossible once $S^1$ is a compact manifold and any differentiable real function on compact manifolds must have critical points.