Obviously, positive semi-definite operators always admit a positive trace as ${\rm tr}(A)=\|A\|_1\geq 0$ whenever $A\geq 0$. This motivates the following "lifted" question:
Given any positive, linear map $\Phi:\mathbb C^{n\times n}\to\mathbb C^{n\times n}$ is it true that ${\rm tr}(\Phi)\geq 0$?
For this recall that the trace of a linear map $\Phi:\mathbb C^{n\times n}\to\mathbb C^{n\times n}$ is defined to be ${\rm tr}(\Phi)=\sum_j{\rm tr}(G_j^\dagger\Phi(G_j))$ where $\{G_j\}_j$ is any orthonormal basis of $\mathbb C^{n\times n}$ (equipped with the Hilbert-Schmidt inner product). As an example one could choose the standard/computational basis $\{|j\rangle\langle k|\}_{j,k}$ and obtain the explicit expression ${\rm tr}(\Phi)=\sum_{j,k}\langle j|\Phi(|j\rangle\langle k|)|k\rangle$. Equivalently, the trace of $\Phi$ is of course equal to the trace of any matrix representation of $\Phi$—such as the natural representation or the Pauli transfer matrix—and the trace is also equal to the sum of all eigenvalues of $\Phi$. To give an example the transposition map $T$—the prime example of a positive but not completely positive map—has trace zero which is in agreement with the above question.
For the special case where $\Phi$ is completely positive the above statement holds as a consequence of the Kraus representation $\Phi=\sum_lK_l(\cdot)K_l^\dagger$: \begin{align*} {\rm tr}(\Phi)&=\sum_{j,k}\langle j|\Phi(|j\rangle\langle k|)|k\rangle\\ &=\sum_{l,j,k}\langle j|K_l|j\rangle\langle k|K_l^\dagger|k\rangle\\ &=\sum_l|{\rm tr}(K_l)|^2\geq 0 \end{align*} As an aside the trace of a channel also represents the mean operation fidelity (cf. Chapter 10.5 in Bengtsson & Zyczkowski's book "Geometry of Quantum States" / alt link) and it can be recovered as an expectation value via ${\rm tr}(\Phi)=\langle \eta|\mathsf C(\Phi)|\eta\rangle$ where $|\eta\rangle:=\sum_j|j\rangle\otimes|j\rangle$ is the (unnormalized) maximally entangled state and $\mathsf C(\Phi)$ is the (unnormalized) Choi matrix of $\Phi$, cf. Lemma 2 in this paper for a slightly more general statement. However, this proof technique doesn't really help us as it does not generalize to arbitrary positive maps.
(This is a Q&A style question meant as a contribution to the list of counterexamples in quantum information)