The 2nd book was still very early in the series, and harry doesn't know much about voldemort except he's beaten him from the previous book.
If you read the next lines:
Dobby shook his head, his eyes wider than ever.
"Well then, I can't think who else would have a chance of making horrible things happen at Hogwarts," said Harry. "I mean, there's Dumbledore, for one thing - you know who Dumbledore is, don't you?"
Harry knows only Voldemort is powerful enough to make trouble in the wizarding world, and he has already defeated him again, and based on his 12 year old (Harry was only 12 in his 2nd year at hogwarts) child's logic, only an individual that is very much close physically to Voldemort (a hypothetical brother) is the best assumption.
The "brother" was just a guess.