Due to the good relations between Sony and Marvel and the deal that they made, Spider-Man seems mostly safe for the moment. Once he enters the MCU, his profile will most likely go up even more.
That being said, I can't help but wonder if he is somewhat in danger of suffering from the fates currently afflicting the X-Men and F4 franchises. Back when the ASM movies were being made, I was seriously worried that Marvel was going to gradually begin to sabotage the franchise and sideline it in favor of stuff like the Avengers. While this probably won't happen now, there is evidence that characters who aren't one hundred percent part of the Marvel/Disney sphere do suffer somewhat. For example, there has been talk that the eradication of the other gamma heroes was due to Hulk being partly under the control of Universal. Disney has a history of being very possessive of its intellectual property, and if Spider-Man is only half theirs, even in a minor way, I fear his world could suffer some cutbacks as well.
One last thing that I will mention is that when the first X-Men film came out, it looked like Marvel could not have been happier. Free Wolverine comics were handed out at theaters, and there were prequel comics detailing the histories of the movie characters. Now look where things are. If, for some reason or another, relations with Sony go south, Spider-Man could get caught in the crossfire.