Why was it initially thought that Mendel's findings were contradictory to Darwin's natural selection?
It's thought that Mendel's communications were anti-Darwinist, and some argue that his original paper was written specifically as a refutation of Darwin's descent with modification. Mendel believed species were created by God and not Darwinian evolution. Because of this, when he found a law defining constant probabilities of heredity, he saw it as more of an argument for the consitency of genetic information and thus species. To him this was in contrast to the ability of heritable traits to vary slightly in progeny, leading to selective advantages. Source I paraphrased: http://jhered.oxfordjournals.org/content/87/3/205.full.pdf