Decentralised social media platforms are increasingly being recognised as viable alternatives to their centralised counterparts. Among these, Mastodon stands out as a popular alternative, offering a citizen-powered option distinct from larger and centralised platforms like Twitter/X. However, the future path of Mastodon remains uncertain, particularly in terms of its challenges and the long-term viability of a more citizen-powered internet. In this paper, following a pre-study survey, we conducted semi-structured interviews with 16 Mastodon instance administrators, including those who host instances to support marginalised and stigmatised communities, to understand their motivations and lived experiences of running decentralised social media. Our research indicates that while decentralised social media offers significant potential in supporting the safety, identity and privacy needs of marginalised and stigmatised communities, they also face considerable challenges in content moderation, community building and governance.