Is it permissible to write articles for someone who will publish them online and place advertisements on them that may include indecent content, in exchange for a fee, or is that considered aiding in sin?

There is no harm in writing articles and earning money for them, as long as they are free from unlawful content and their publication does not serve an unlawful purpose. If others publish them on the internet and place unlawful advertisements on them, this does not make your writing or earning money unlawful, nor does it mean you are assisting them in what is forbidden.