The meaning is basically the same, but I think 'You are not allowed to be late' suggests that there will be consequences or a punishment if you are late.

"You can't be late." also has the sense of: You 'shouldn't be late', or basically 'don't allow yourself to be late'. "You are not allowed to be late.", means that 'others' who have the right or authority are saying: You should not be late.

1) You can't be late. - uses in speaking (informal conversation) 2) You are not allowed to be late. - sounds like a rule. If you disturb this rule you might be punished.