var = queue.isEmpty();
if(var=true) // this line *sets* var to true
{
    System.out.println("queue is empty");
}

If you change if (var=true) to if(var==true) or just if(var) you should see a different result

To begin with, use a consistent way of passing your queue around. Note the differences in the interfaces:

int isEmpty(Queue);             //<-- by value
void enqueue(Queue*, char);     //<-- by reference
char dequeue(Queue*);           //<-- by reference
void printQueue(Queue);         //<-- by value
void freeQueue(Queue*);         //<-- by reference

Some of these are passing a Queue structure by value, and others by reference (pointer). It's likely that you want all your functions to operate on a pointer, i.e. Queue*.

Next, you should have some kind of operation that initializes the queue. You have freeQueue already, which does the inverse. So you probably want something like initQueue:

void initQueue(Queue* q) {
    q->head = NULL;
    q->tail = NULL;
}

Now, on to the actual question... As I've already suggested, you should change isEmpty (and printQueue) to accept a pointer to the queue. And then you use whatever logic should indicate the queue is empty. Since I've asserted above that on initialization, the head pointer should probably be NULL, then that would be an appropriate "empty" test as well:

int isEmpty(Queue* q) {
    return q->head == NULL;
}

And finally, since you're likely to ask how to actually use this:

int main(void)
{
    Queue q;

    initQueue(&q);
    printf("Queue empty: %d\n", isEmpty(&q));

    enqueue(&q, 'X');
    printf("Queue empty: %d\n", isEmpty(&q));

    enqueue(&q, 'Y');
    enqueue(&q, 'Z');
    printQueue(&q);

    printf("Removed %c\n", dequeue(&q));
    printQueue(&q);

    freeQueue(&q);        
    return 0;
}

Assuming you mean Queue<T> you could just use:

if (queue.Count != 0)

But why bother? Just iterate over it anyway, and if it's empty you'll never get into the body:

Queue<string> queue = new Queue<string>();

// It's fine to use foreach...
foreach (string x in queue)
{
    // We just won't get in here...
}