First of all, as pointed out in the comments, you need to match lines starting with a #, since there are multiple lines beginning with # but having a different second character.
Next, you need to check the value of the line that you are reading to check for the # character. So, you can get rid of the firstHandler
variable and use the line
variable instead.
Finally, you need to get rid of the break
statement, since that causes the loop to exit after the first line itself. That is the reason you only see the first line on the screen.
Therefore, your code can be changed to something like this:
while ((line = bufferedReader.readLine()) != null)
{
if (line.startsWith("#"))
{
System.out.println(line);
String[] parts = line.split("=");
System.out.println(Arrays.toString(parts));
}
}