It's a matter of principle.
On one hand, the atheist may consider himself to know Catholicism without being Catholic, due to having a superior level of education.
On the other hand, in this sense, imagine different synonyms for educated. Informed, knowledgeable, even intelligent. Informed, is in a similar situation; the atheist may try to assert superiority, or just may be aware of Catholic traditions. Knowledgeable is less assertive, by implying a broad level of knowledge. Using intelligent instead of educated definitely implies superiority, however. In that regard, he would be claiming that the Catholic is not intelligent, because they are Catholic. It gives a prejudicial overtone.
"Well educated" would be a far better term to use instead, as, much like knowledgeable, it would imply intellect in a wide variety of areas, not just claiming higher levels of intelligence over another person.