In last night's episode, Booth (David Boreanaz) proposed to Hannah (Katheryn Winnick) but was rejected.
"Brennan was shot down [by Booth], then Booth was shot down by Hannah," Nathan told TV Line. "If they then all of a sudden fall into a relationship together, I don’t think anybody’s going to believe that. It would just be a TV conceit. It wouldn’t have any real truth to it."
He added that the crime-solving duo will reestablish their friendship following recent events.
"Both of them are gun-shy, and the one thing that both of them have to rely on is their friendship," he said. "That’s the thing that’s going to sustain that relationship."
He also claimed that a union between Booth and Brennan could prove divisive among fans of the show.
"There were a lot of people screaming and yelling about [House and Cuddy's romance on] House," he claimed. "For as many people who are disgruntled and unhappy by an event like that, there will be an equal number, if not more, happy about it.
"But we’re taking our time. Hopefully we’ll be around for a few more years, so we’ll see how that [storyline] unwinds."
Bones airs on Thursdays at 9/8c on Fox.