Data-driven algorithms can adapt their internal structure or parameters to inputs from unknown application-specific distributions, by learning from a training sample of inputs. Several recent works have applied this approach to problems in numerical linear algebra, obtaining significant empirical gains in performance. However, no theoretical explanation for their success was known. In this work we prove generalization bounds for those algorithms, within the PAC-learning framework for data-driven algorithm selection proposed by Gupta and Roughgarden (SICOMP 2017). Our main result is an almost tight bound on the fat shattering dimension of the learning-based low rank approximation algorithm of Indyk et al. (NeurIPS 2019). Our techniques are general, and provide generalization bounds for many other recently proposed data-driven algorithms in numerical linear algebra, covering both sketching-based and multigrid-based methods. This considerably broadens the class of data-driven algorithms for which a PAC-learning analysis is available.