Hypergraphs capture the higher-order interactions in complex systems and always admit a factor graph representation, consisting of a bipartite network of nodes and hyperedges. As hypegraphs are ubiquitous, investigating hypergraph robustness is a problem of major research interest. In the literature the robustness of hypergraphs so far only has been treated adopting factor-graph percolation, which describes well higher-order interactions which remain functional even after the removal of one of more of their nodes. This approach, however, fall short to describe situations in which higher-order interactions fail when any one of their nodes is removed, this latter scenario applying, for instance, to supply chains, catalytic networks, protein-interaction networks, networks of chemical reactions, etc. Here we show that in these cases the correct process to investigate is hypergraph percolation, with is distinct from factor graph percolation. We build a message-passing theory of hypergraph percolation, and we investigate its critical behavior using generating function formalism supported by Monte Carlo simulations on random graph and real data. Notably, we show that the node percolation threshold on hypergraphs exceeds node percolation threshold on factor graphs. Furthermore we show that differently from what happens in ordinary graphs, on hypergraphs the node percolation threshold and hyperedge percolation threshold do not coincide, with the node percolation threshold exceeding the hyperedge percolation threshold. These results demonstrate that any fat-tailed cardinality distribution of hyperedges cannot lead to the hyper-resilience phenomenon in hypergraphs in contrast to their factor graphs, where the divergent second moment of a cardinality distribution guarantees zero percolation threshold.