But Neilson insists: “John is one of our best players so he will be available for selection until things change."
Souttar remains a Hearts players until the summer, unless the club accept an offer from Rangers to take him to Ibrox before the end of the January transfer window.
Rangers manager Giovanni Van Bronckhorst has indicated that he is willing wait until the summer for Souttar, but a bid is still expected from the Ibrox club before the end of the month.
Van Bronckhorst said: "We have to wait on what will happen in this window, but as far as I know we welcome John in the summer."
Ahead of the home cinch Premiership game against bottom side St Johnstone, where Hearts resume action after the winter break in third place behind leaders Rangers and Celtic, Neilson was asked what his message was to the Hearts supporters.
"The most important thing is the football club," he said. "Myself, the rest of the players, the staff, everyone, it is support for the club going forward.
"No player is bigger than the club, no player will ever be bigger than the club.
"People will come and go, the most important thing is come and support and help us get the three points for the club.
"I understand the frustrations of fans, there is a disappointment there but at the end of the day it is about winning tomorrow, taking this club forward and trying to get European football which will take us to the next level again.
"The objective is to try to get European football so we have to utilise the squad and play our best players and John is one of our best players so he will be available for selection until things change."
Neilson concedes Souttar's decision to move on is "part and parcel of football".
He said: "We offered John a contract, he decided to turn it down and the way the Bosman rule is he can go and speak to people and we knew he was speaking to clubs and he has decided to go somewhere else.
"I have spoken to John and he understands the situation and he is big enough and old enough that he has to make sure his head is right.
"He has reassured us that he will give 100 per cent in training which he has done and 100 per cent if he is selected.
"Obviously we are disappointed but at the end of the day the club is and always will be bigger than any one player.
"The most important thing is we focus as a club and a team and get ready to win the game tomorrow night and then move forward."
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