It was a reflexive response he had every time someone hugged him - Bruce initially stiffened, but swiftly relaxed into the physical contact. As much as he enjoyed the affection, he had a tendency to hold himself away from it protectively, and had since he was just a little younger than Cassandra. He had worked very hard to get past that barrier for Dick when he was a boy, so Bruce understood how important it was for him to do the same for his daughter now.
Just as it was important for him to let her know that no matter how upset he was, that it didn't change his feelings for her, and he said so: "I love you, too." He had no interest in guilt, just understanding.
And even though he knew exactly why she'd run away, to start their dialogue, he asked her, "Why?"