For a backup, I guess.
Backup? That is like bringing $250 to a street corner when you wanted to purchase a 25 cent gumball?
There was probably no time to build another containment unit to hold the red matter during the trip so it was an all or nothing situation. Remember that when they removed a little sample one the Narada they were extremely cautious with it which shows that the smaller container wasn't enough to protect the sample.