The answer is no. Consider as a counter-example $M = \mathbb{R}^2$, $\omega = dx \wedge dy$, $X = x \frac{\partial}{\partial y}$ (whose Hamiltonian function is $-x^2/2$), $Y = y \frac{\partial}{\partial x}$ (whose Hamiltonian function is $y^2 /2$) and the (symplectic) connection given by usual (i.e. component-wise) differentiation of vector fields. Then $\
abla_X Y = x \frac{\partial}{\partial x}$, which is not symplectic as it is not Hamiltonian (or alternatively because it doesn't have vanishing divergence).