One proof is given in the paper
Noam D. Elkies, Andrew M. Odlyzko, and Jason A. Rush: On the packing densities of superballs and other bodies Invent. Math. 105 (1991), 613-639.
Instead of Fejér-Riesz, we use the Fourier inversion formula directly.
Assume for contradiction that $\phi_k(\xi) \geq 0$ for all $\xi$.
Then for all $x$ we would have
$$
0 \leq \int_0^\infty \phi_k(\xi) \, (1 - \cos (\xi x))^2 \, dx
= \frac12 \int_0^\infty \phi_k(\xi) \, (3 - 4 \cos (\xi x) + \cos (2\xi x)) \, dx,
$$
which means
$$
3 - 4 e^{-x^k} + e^{-(2x)^k} \geq 0
$$
for all $x$. But for $x$ near $0$ we may write
$e^{-x^k} = 1 - \epsilon$ and
$e^{-(2x)^k} = (1 - \epsilon)^{2^k} = 1 - 2^k \epsilon + O(\epsilon^2)$,
so
$$
3 - 4 e^{-x^k} + e^{-(2x)^k}
= 3 - 4(1-\epsilon) + (1 - 2^k \epsilon + O(\epsilon^2))
= (4 - 2^k) \epsilon + O(\epsilon^2).
$$
Thus $3 - 4 e^{-x^k} + e^{-(2x)^k}$ becomes negative for small $x$
once $2^k > 4$, which is equivalent to $k=2$,
and we have our desired contradiction.