As told by everyone here, late coming is not good, especially for HR personnel. Everyone else takes it for granted that HR itself is late. The first thing an employee does when they enter the office is to look at the HR seat to see if HR is in. I have seen that happening daily in my company. When they come in late, they avoid looking at HR to just make themselves believe that they are not late or they want to avoid that sight. So, try to be punctual always. I do understand that there will be situations for everyone, but it should not be a daily occurrence. In those times, make it a point to message your boss that you will be late due to the situation, which should definitely not happen more than twice a month. Your boss is deducting your pay just to ensure that he brings in discipline. He cannot enforce it in others unless his own department first follows it. Else, he will be questioned why his department alone is given the privilege. This, I am sure, you will agree that no boss will want.
This is a great opportunity you have got. No one will get the chance to get into HR, especially as a fresher. Do make the best use of that opportunity. All the best.