Meaning of 点 in 你现在好点了吗？
First of all, 好点了吗 is same with 好一点了吗.  
Yes, the word 一点 means "one o'clock", but also means "a little bit".  Sometimes, we say 一点点 for emphasis, means "liiiiittle bit".

Well, to explain the objective of the question. 
It is NOT asking if your health (or 100 HP) recovered from 50 to 51, which is really "little" 
It is supposed to ask for any progress of recovery, which can be positive news.

Some relative sample sentences here: 
好一些了吗 "一些": some, few, a little. 
好多了 : much better, but normally for replying not asking others. 
好了吗 : 100% recovery of your health (or HP). 
过去一点 or 过去点 : move a little bit.