Okay, I will try to say this nicely.
Given that the data to be read is 1001,11001, etc and given the text The binary number will be passed in as an array of Booleans (a true represents a 1 and a false represents a 0) it seems faairly obvious that you need to create the binary array yourself. It's a stupid requirement, yes, but that's the way the world is. I've seen requirements much worse in real projects.
Now, maybe it's just me, but that all seems to be glaringly obvious, so your first post said to me (reading between the lines), "write (at least this part of) the program for me". Which was the reason for my first post. I apologize if that was not the case, but that is the way I interpreted the first post (and we get that here so often it has become the norm, rather than the exception).
But, in any case, read in the String, create a boolean array of the same length as the String, then loop over the String setting each element in the array according to the requirements provided in the assignment text. (Really, you only need to worry about the ones, as a boolean array is initiated with all elements false, which is how 0 is to be represented.)
Edit: And a boolean is, yes, a boolean. But, what is a boolean? It is a switch, an "either/or", in other words, which is also exactly what a bit is. It uses 1/0 as the textual representation, whereas a boolean uses true/false, but they mean the same thing, on/off or used/free. That is another way of seeing a boolean, and what, I believe, is meant here.