Cassano has been left out of Samp's squad for the last three Serie A games, leading to speculation of a problem between coach Gigi Del Neri and the former Roma star.
"The relationship between Cassano and Del Neri is based on reciprocal respect and professionalism," said Marotta.
"His exclusion is a technical choice and there are no disciplinary reasons behind it."
Cassano's absence has not hindered Samp, who have won their last three league games, including last weekend's 2-1 win at Siena to climb to sixth in the standings.
The temperamental playmaker turned down a move to Fiorentina earlier this month and it remains to be seen when he will return to action.
"Cassano is a natural-born talent," said Marotta.
"Even if we have won our recent games without him, his presence and quality will help Sampdoria."