It is the second time Samba has been dismissed this season and Allardyce claims his player is not getting the rub of the green.
Allardyce said: "We will lose Chris for two vital games after an unjust decision.
"When you see some of the tackles that went unpunished last weekend, he was unfairly treated.
"Because there is no form of appeal, you are harshly punished again for something that should not have happened.
"I did a bit of research and it seems big boys get booked more than the smaller ones. That is going to go against Chris as he is 6f 5in and he can't hide anywhere."
When Samba was sent off against Aston Villa earlier in the season, Blackburn responded by beating Wigan.
Allardyce would like a similar reaction against Hull.
He said: "Chris is very dominant as a defender as well as giving us a presence in the opposition box and we will miss him.
"It is a great shame for us but something we have to get over. We managed it before when he was sent off against Villa.
"Now we have got to try and do that against an in-form and confident Hull side."
Lars Jacobsen and Vince Grella could return to the squad after thigh injuries.
Both players had a run-out for the reserves at Fleetwood last night as did new signing Yildiray Basturk.
While Blackburn were losing to Stoke, Hull followed their draw with Chelsea by defeating Manchester City.
Allardyce knows they will have their work cut out against a side managed by his former assistant at Bolton, Phil Brown.
"They are in the top form teams in the country and it is probably the wrong time to be playing them, " said the Blackburn boss.
"But we have a really good home record and that must continue. We want to get to the 30-point mark as that will mean we need single figures to secure our status."
Blackburn will mark the death of a supporter when they face Hull.
There will be a minute's silence before the match with players wearing black armbands out of respect to John Steven Taylor.
He died of a head wound while attending the game against Stoke on Saturday at the Britannia Stadium.
Allardyce said: "It is a great tragedy that has happened. I have never heard anything like this in my entire life. It is a great shame.
"Our sympathies go out to his family and we will doing our utmost in terms of respect for him.
"If it helps the family in some way, we will get them a win and three valuable points."
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