No, this isn't the case. Generally speaking, ovulation occurs primarily at a point in the cycle that is quite favorable to implantation---when the uterine wall is well-prepared. So the primary effect of the rhythm method is to prevent conception, not implantation.
I do believe that it is possible for a woman to ovulate outside of that time frame on occasion. I've heard it can be in response to some stimulus (like sex) or spontaneous. I guess in that case there is a lower chance of implanation. But someone practicing the rhythm method isn't necessarily encouraging this phenomenon any more than someone who is not.
Someone please correct me if I'm wrong.