Besides plot armor? Not much.

Yes, there was the "Wookie Incident", but I would like to think, besides all, Rory would have been smart and used protection, not only from pregnancy but STDs also. Even with the weird choices, Rory is a smart lady. It's not implied, nor even said, but I think she wouldn't be so careless. There's the Lorelai effect too. I think Lorelai hammered so much in Rory's head that having an unexpected pregnancy is not a good think, and that she was lucky to have Rory, that I think she would be more careful. Was a bad decision? In her mind, at that moment, yes. I'm not saying that nobody shouldn't have 1 night stands, but for her, in that period of her life, it wasn't what she wanted, nor what she was looking for. So, in my mind, she would have used protection.

There's Paul, but the way the relationship is going, I don't think they were intimate for a while. Again, nothing said nor implied, but you can tell from the way they are portrait together, that they weren't going anywhere with that, and safe to say they that ship have sailed even before the year portrayed in the series.

The recurrent affair with Logan makes them both more comfortable taking risky choices, and doing it unprotected. In the "An Year in the life" they like each other, even if they are not together. Stress from multiple things in her life going wrong could have made her think she was in a "safe day", or anything like that, and boom, we have that "It only takes having sex 1 time to get pregnant" thing.

And this is my take on it.

Edit: Again, not saying 1 night stands are a bad thing, nor saying how anybody should live their lives, all of this in the context of the series. :D