What's fair is what you two decide between you is fair. Why don't you talk to your baby daddy instead of asking random strangers on an international message board?
Very foolish to have a baby when you are not in a committed marriage, with the legal protections for a child of the marriage. So you need to hire an attorney & get a court order of child support.
He should at lest pay for half of the rent.
If he just got a job he's probably not going to be able to afford 3 months rent.
If you want him to pay you back then you should discuss that with him.
When you moved in together, you KNEW he did not have a job, so it was EXPECTED that you pay the rent.
Unless you two had an adult conversation about your living expenses, it is hard to say what you guys talked about in regard to your finances.
I suppose you can ask him to pay the rent for three months and then split it after that timeframe. If he was a gentleman, he would pay the next three month's worth of rent by himself.
If your name is on the lease, you are legally responsible to pay all the rent. If he does not pay, then he should live elsewhere if you are not willing to financially support him and your child.
You should never have let him move in without being married to you. When you are married your earnings become joint. That means it does not matter who pays the rent. You draw up a budget that shows how much money you have coming in and how much you need. If there is anything left over, you put some that into a saving account in case one of you loses his job. Anything else can be spent on discretionary stuff like a television, shoes, a beer on Saturdays or a holiday.
You should also not have had a child until you had the above sorted out but too late to do anything about that now. You might take a good hard look at this man. If he is not marriage material, now is the moment to chuck him out although rearing a child alone is not for the faint hearted.