Certainly, there are Spanish native speakers who can't roll the r, but this is not a common problem and rarely represents a difficulty to children.
According to logopedics (logopedia) — the study, and correction, of speech defects, especially in children —, this is called "rotacismo" or "dislalia del fonema r".
Dislalia is classified as a speech disorder. It sounds very weird to native Spanish speakers and according to logopedists it can lead to low self-esteem, social isolation and even statter.
If you allow me to add a personal anecdote here, I've only heard a handful of native speakers having difficulties to roll the r in my whole life, and in this particular moment I can't even remember a person among friends, relatives, students, teachers, colleagues etc... who has this problem.
Please note that even if there are regions where the r is not rolled (some evidence here would be welcome) does not invalidate this truth: that not being able to roll the r in the same way as the rest of the population is a rare phenomenon and of course considered a speech impediment, which can most of the times be corrected by a logopedist.
Please also note that rolling the r is not exclusive to Spanish. Other languages, such as Russian, Polish and German as spoken in Bavaria, roll the r in (nearly) the same way. The same that we are discussing here applies to those languages.