Since last season replays have been scrapped from the first round onwards, meaning clubs such as Exeter do not get the chance of a second pay day should they earn a draw.
Last season, the Grecians were knocked out in the fourth round on penalties by Nottingham Forest, missing the chance of a lucrative replay at the City Ground having drawn 2-2 after extra time.
Exeter received a massive boost in 2005, when they were a non-league club with millions of pounds of debt, when Manchester United gave them all the gate receipts from their 0-0 third-round draw at Old Trafford, with the Premier League side progressing in a televised replay.
“We just wanted to flag up to the football world about how the smaller clubs can be penalised in the FA Cup now,” chairman Pete Ferlie told BBC Radio Devon.
The trust has put in further loans worth more than £600,000 this season after an overspend last year left the club with worrying debts.
They were then hit by a fire in November, which caused more than £100,000 worth of damage and led to a League One game being postponed on safety grounds.
“Money is tight at the moment, but we have worked our way through that,” added Ferlie.
“There are actions and plans being put in place to put the situation back on a more even keel.
“This extra money from the FA Cup helps, of course it does, but we would like to see a little bit more to really make sure that the summer is easier than it could be.”