While there have been reports of behind the scenes conflict between Marvel and FOX, which came to a head over the "dueling Quicksilvers", it appears as though the relationship with Sony is very strong. The two studios cut a deal back in 2011 in which Marvel paid $278 million for Sony's share of the Spider-Man Joint Venture and also gave up their remaining interest in Sony's Spidey movies. Sony also released the Ghost Rider rights immediately after the sequel flopped, as opposed to FOX which had clung to Daredevil and now the FF until the bitter end.
Though Marvel has not provided movie tie-in merchandise for the X-Men franchise subsequent to the Disney purchase, the Mouse had fully supported the last two Sony releases, and this March will be putting out an "Art Of" book for TASM, the first for a non Marvel Studios release. They also came close to collaborating on an Avengers movie easter egg, with OSCORP making an appearance in the skyline.
So while Marvel would certainly love having Spidey's movie rights, they are making lots of money from merchandise - Spider-Man is tops among superheroes in licensing revenue - animation, video games and the like. So long as both studios are raking in the dough, the relationship will be fine.
