It is common and correct to say that the moral message in the Pardoner's allegory is that money brings all evil.
Anyway, it is important to perceive the discrepancy between what Pardoner says and his behaviour. A Pardoner is a person who offers indulgences. Indulgences were the way to obtain forgiveness for sins and the direct ticket to enter heaven in exchange of a monetary contribution for the Church. Pardoners were supposed to be offering help, spiritual help in this case, but actually pardoners were taking profit of poor peasants and pilgrims.
The Pardoner told the pilgrims a tale about the miseries that money greed brings, and right after he tried to sell relics as indulgences. So actually, the moral message in the allegory is double, because this situation exemplifies how those who praise morality should be watched over carefully.
