We consider the facility location problem with submodular penalties (FLPSP) and the facility location problem with linear penalties (FLPLP), two extensions of the classical facility location problem (FLP). First, we introduce a general algorithmic framework for a class of covering problems with submodular penalties, extending the recent result of Geunes et al. (Math Program 130:85-106, 2011) with linear penalties. This framework leverages existing approximation results for the original covering problems to obtain corresponding results for their counterparts with submodular penalties. Specifically, any LP-based α-approximation for the original covering problem can be leveraged to obtain an 1 − e −1/α −1 -approximation algorithm for the counterpart with submodular penalties. Consequently, any LP-based approximation algorithm for the classical FLP (as a covering problem) can yield, via this framework, an approximation algorithm for the counterpart with submodular penalties. Second, by exploiting some special properties of submodular/linear penalty function, we present 123 Algorithmica an LP rounding algorithm which has the currently best 2-approximation ratio over the previously best 2.375 by Li et al. (Theoret Comput Sci 476:109-117, 2013) for the FLPSP and another LP-rounding algorithm which has the currently best 1.5148-approximation ratio over the previously best 1.853 by Xu and Xu (J Comb Optim 17:424-436, 2008) for the FLPLP, respectively.