Owners the British Racing Drivers' Club says it cannot afford to host the race after 2019 unless a new deal is agreed.
Horner says the decision to exercise its break clause risks the race being moved to a London street track.
"They signed a contract. They knew what they were entering and they've now realised they can't afford it, despite having a full house every year."
He added: "They either shouldn't have signed it in the first place or they got their maths wrong."
The BRDC had a contract until 2027 but it contained a break clause to end the deal after 2019 which had to be activated before this year's race this weekend.
Silverstone sought to reach a compromise agreement with F1's new owners Liberty Media but these talks failed.
Liberty offered a series of options to try to help Silverstone but the track believed these were not satisfactory.
Media playback is not supported on this device
F1 is hosting an event in London on Wednesday, with all the teams and many drivers taking part in a demonstration at Trafalgar Square.
Horner is a member of the BRDC but said he did not involve himself in any club decisions.
He added: "Liberty have made a commitment that there'll be a British Grand Prix but with this London event happening, if that was a success - which hopefully it should be - with the recent legislation changes there have been in the City of London, you can imagine a London grand prix being pretty attractive to the Liberty guys.
"So Silverstone need to be a little bit careful how they handle themselves and negotiate, that they don't find themselves losing out. I'm amazed they have triggered their break clause."
John Grant, the BRDC chairman, dismissed the idea of a street race in London.
"Most informed observers would say a London event is just not feasible - politically, environmentally or commercially," he said.
Horner added: "From Liberty's perspective this is a historic problem rather than something recent. Silverstone get favourable rates anyway. It is hard to imagine they lose money putting 120,000 people in there, plus all the corporates and everything else during the course of the weekend.
"I'd question how it's been managed and the negotiation they had in the first place."
Grant said Silverstone had "sustained losses of £2.8m in 2015 and £4.8m in 2016, and we expect to lose a similar amount this year".
The current contract was negotiated by a previous management team, which left the track under a cloud a few years ago.
It started at £12m in 2010, but costs £16.9m this year and would have been £27.5m in 2027 had Silverstone not exercised its get-out clause.
The contract was predicated on updates to the track, including a new pit and paddock complex, but Horner said these had been badly executed.
"They spent a fortune on the pits and put them in the wrong place," he said.
"They've created a paddock that has zero atmosphere at one of the most historic race tracks in the UK so there was some serious misjudgement and management, one would say.
"But it is the British Grand Prix and Britain should absolutely have a grand prix. But there have been some questionable calls made.
"It would be shocking to lose Silverstone from the calendar and even more shocking to lose a British Grand Prix when you consider 80% of the teams are based within the UK and how much the UK contributes to F1 from a historical point of view."
Red Bull team boss Christian Horner says he is "amazed" Silverstone has ended its British Grand Prix contract.