Oh yeah, of course they want to keep him! I don't mean they wanted rid, that would make no sense at all.
They clearly think he's good, I'm talking about just how good though. As far as i'm aware we weren't batting off interest from Leicester and Wolves, nevermind Bayern, Barcelona and Real Madrid, in order to get him to sign a contract. The only PL team I saw mentioned was Newcastle, which is an obvious one. That suggests he isn't necessarily seen in football circles as likely to be a superstar in the next 12 months. The length of contract is an indicator too. There doesn't appear to have been any great rush to tie him to a long term contract as soon as we could, which is what usually happens when you're totally convinced on a player. All the reports when he signed the contract also suggested he was going to be loaned again next season; there was a lot of talk about them giving him a development map that he was happy with, rather than assurances that he would be getting game time.
None of that is a reflection of his long term prospects. I'm not saying they don't think he'll ever be really good, just that the indications are that they may be slightly hedging their bets in the short term. Holgate is just starting to come good now at 23, and even he can still look a bit of a defensive novice at times. Expecting a 20 year old to come in and be able to play centre half at the top level is a big ask I think. If he's capable of doing it then we should get him tied down long term ASAP, because that would suggest he's potentially top class.