In a modeling paper I am writing, I know that there are some limitations.
Is it a bad idea to point out the limitations? Am I just giving the reviewers more straw for them to reject my paper?
Science is not about getting papers published; it's about writing papers that move a field forward. So don't let worries about reviewers prevent you from adding content that you feel should be there. Indeed, modeling papers that hide their limitations are much less effective at advancing a field than those that clearly explain them.
Good reviewers recognize this and often look in the Discussion for a clear exposition of the model's limitations as well as its strengths. That said, to be worth anything a model must make useful contributions despite these limitations, and it's your job to explain how your model does that.