Will my 7 month old maine coon ever be nice to my maltese puppy?

I got my puppy on thurs. besides him being very very sick he is 100% better now. My maine coon kitty has not gotten used to him at all. He swats him & bites him even when I am holding the puppy. Im scared to let them loose in the same room. My kitten waits by the door and puts his paws under the door and swats around for hours. I understand he might feel alittle pissed off that this little guy is in his house.. But he hasnt been nice not one bit. The puppy just wants to play & play of course, has no idea that he thinks of him as the enemy. Anyone ever have this problem with there kitty? How long will it be like this? Will he ever get used to him or am I always going to have to keep them in seperate rooms?