The study of Markov processes and broadcasting on trees has deep connections to a variety of areas including statistical physics, graphical models, phylogenetic reconstruction, Markov Chain Monte Carlo, and community detection in random graphs. Notably, the celebrated Belief Propagation (BP) algorithm achieves Bayes-optimal performance for the reconstruction problem of predicting the value of the Markov process at the root of the tree from its values at the leaves. Recently, the analysis of low-degree polynomials has emerged as a valuable tool for predicting computational-to-statistical gaps. In this work, we investigate the performance of low-degree polynomials for the reconstruction problem on trees. Perhaps surprisingly, we show that there are simple tree models with $N$ leaves and bounded arity where (1) nontrivial reconstruction of the root value is possible with a simple polynomial time algorithm and with robustness to noise, but not with any polynomial of degree $N^{c}$ for $c > 0$ a constant depending only on the arity, and (2) when the tree is unknown and given multiple samples with correlated root assignments, nontrivial reconstruction of the root value is possible with a simple Statistical Query algorithm but not with any polynomial of degree $N^c$. These results clarify some of the limitations of low-degree polynomials vs. polynomial time algorithms for Bayesian estimation problems. They also complement recent work of Moitra, Mossel, and Sandon who studied the circuit complexity of Belief Propagation. As a consequence of our main result, we show that for some $c' > 0$ depending only on the arity, $\exp(N^{c'})$ many samples are needed for RBF kernel regression to obtain nontrivial correlation with the true regression function (BP). We pose related open questions about low-degree polynomials and the Kesten-Stigum threshold.