First, it should be noted that the story of the 95 Theses being nailed to the door of the Wittenberg cathedral is an urban myth. The theses, following standard procedure for the period were disputed at the University of Wittenberg.
These theses were aimed at what Luther perceived as the corruption of the Roman Church of the period. His first major concern was the doctrine of works of supererogation and concomitant selling of indulgences. In Roman Catholic practice of the period, saints were assumed to have committed good deeds beyond those necessary for their own salvation, leaving a pool of merits that the church could redistribute to help others buy off years in Purgatory; the Church used this to raise money from rich donors.
Other things Luther advocated were communion in both kinds for the laity and wide access to vernacular Bibles.