Good question. From what I've read, it's hard to know. Some pronunciation can be reconstructed with relative certainty due to misspellings, rhyming/poetic meter, etc., but I'm not sure if that applies to trilled vs. untrilled R's. Most Classical Latin pronunciation (and Ecclesiastic Latin, for that matter) calls fro trilled R's; it is my understanding that this is based on the prevalence of trilled R's in Romance languages.
So generally, yes.
But of course, I'm not an ancient Roman.