Approximate Message Passing (AMP) algorithms have seen widespread use across a variety of applications. However, the precise forms for their Onsager corrections and state evolutions depend on properties of the underlying random matrix ensemble, limiting the extent to which AMP algorithms derived for white noise may be applicable to data matrices that arise in practice. In this work, we study more general AMP algorithms for random matrices $W$ that satisfy orthogonal rotational invariance in law, where $W$ may have a spectral distribution that is different from the semicircle and Marcenko-Pastur laws characteristic of white noise. The Onsager corrections and state evolutions in these algorithms are defined by the free cumulants or rectangular free cumulants of the spectral distribution of $W$. Their forms were derived previously by Opper, Çakmak, and Winther using non-rigorous dynamic functional theory techniques, and we provide rigorous proofs. Our motivating application is a Bayes-AMP algorithm for Principal Components Analysis, when there is prior structure for the principal components (PCs) and possibly non-white noise. For sufficiently large signal strengths and any non-Gaussian prior distributions for the PCs, we show that this algorithm provably achieves higher estimation accuracy than the sample PCs.