Not all royals are buried at Frogmore. Queen Victoria's youngest daughter Princess Beatrice isn't, she's buried on the Isle of Wight. Various other British royals are buried in assorted church yards around the UK. Included there, are estranged spouses of royals, their spouses were buried at Frogmore they weren't. Princess Alice ( Prince Philip's mother, therefore grandmother of a future king, great-grand-daughter of a Queen ( Victoria), herself born at Windsor Castle died in Buckingham Palace isn't buried at Frogmore. She's in Jerusalem, interred with her aunt Grand-Duchess Elizabeth) It's not an automatic thing, that you're a member of the royal family so you'll be buried at Frogmore. William and Harry and their future families could just as easily choose not to be.
The Queen didn't give the option that Diana could be buried at Frogmore, she originally passed the whole dealing with Diana's funeral arrangements over to the Spencer family. Charles had to insist just so Diana's casket could be kept at the chapel at St James's, it had been scheduled once it arrived in the Uk to be kept in the funeral home. The Spencers would be responsible as to where Diana was buried. Earl Spencer didn't have to insist on anything, the Spencers could have placed her in the family vault but there was the issue that the church was small. Also at the time too with the mass hysteria was the issue of crowds, the worshipper's shrines and not to mention potential desecration and vandalism of Diana's grave. ( Not everyone was a fan)
Earl Spencer came up with a most appropriate solution, Diana would be buried at Althorp on an island where the public had no access, that way her grave would be protected and family members who wished to visit her grave could do it in total privacy without strangers around them. He gets criticised for "profitting from Diana" but Althorp is only open from July 1st to Aug 30th ( this year because of the 10th anniversary of Diana's death, it's open July 2nd to Sept 2nd) each summer, unlike all other stately homes in the UK which are open to the public from April to October. The official site for Althorp has no large pictures or banners of Diana and only one sentence on the site mentioning the display. He makes most of his money from the corporate events he stages and as well as events such as a book festival and the staging of plays. With fewer people interested in Diana the visitor numbers to the Diana exhibition have dropped off, it was never a major moneyspinner ( or attraction) as he had to renovate the stable area to put in the exhibition.
Diana herself identified strongly as a Spencer, once her marriage went sour, she deliberately chose to wear the Spencer Tiara to official events and not the Cambridge lover's knot tiara the Queen gave her. She pointedly wore 'her' tiara, which was somewhat inconvient as everytime she wanted to wear the Spencer tiara it had to be taken out of the bank vault where it was kept and then transported to Kensington Palace.
Ok so she was the mother of a future king, but she was also the divorced wife of a future king, that alone would have her buried somewhere else. If she had remarried she wouldn't even have had the 'princess of wales' part in her name. There were many princesses of wales, it wasn't a title solely identified with Diana, hearing Princess of Wales I tend to picture Queen Alexandra who was probably the most famous of them.
I doubt whether William would ever have her reburied at Frogmore, there would be no point and as I said before, royals are buried at other sites in the UK.
She is not a Queen in everyone's heart, but she is in mine, and I think some (like the Truth) will feel the same. 
