I am optimistic about this.
ATLUS would have to localise their games to Europe in a timely fashion for starters, since it's SEGA's biggest region for profits.
In addition to this, SEGA has an established JRPG IP in SMT and Persona, in addition to a unique genre from Trauma Centre.
The only downside is that I don't believe ATLUS' games don't sell THAT well, at least for SEGA.
I can see ATLUS' Etrian Odyssey series being put on a back burner for 7th Dragon (but isn't that a good thing if SEGA localises it?), and Vanillaware using SEGA as a publisher for their games too.
ATLUS fans are concerned as SEGA aren't good at advertising, but I believe ATLUS grew their fanbase from Persona 4 and it didn't really budge since...so whoever buys their games already will.
I understand the concerns from most people, but I could see ATLUS retaining their division for having a brilliant record of creative games that sell well, it's up to SEGA to decide if they could make money off of them now.
Not sure if SEGA would own Madhouse though...but we shall see.
By the way, I am not a fan of ATLUS in any way, shape or form...I can blame being european for this but meh...they're games aren't as interesting for me.