I'd say showing that some humans still believe in deities and/or participate in religion goes with the general thrust of showing how humanity has grown enough to at least deal successfully with several deeply-rooted flaws that remain. It's a more realistic angle on Trek's optimistic view of the future - there's the simple version where humanity has generally just improved, and the more nuanced view where it has grown up enough to deal with internal strife in a constructive manner on a species-wide scale. Realistically, there's just relatively little hope of abolishing religion in the time frame we're speaking about. It's a powerful meme, and recently there seems to be some scientific basis to at least consider that a large percentage of the population may be psychologically set up to gravitate to such ideas.