The reason for why the grave of Imam Ali (as) was concealed for a while was the fact that ignorant and abusive individuals who were enemies to him, would possibly disrespect his grave. Later on though, after time had passed and the abovementioned individuals had passed away, in addition to the growing strength of the school and teachings of the Ahlul-Bayt, the possibilities of such a matter lessened. Moreover, since the grave was located in between reeds and the desert, no one was certain even about its approximate whereabouts, causing the people not to be able to visit it and from its great blessings and bounties. These factors caused the imams to show the grave to their true followers and slowly, it became known to all over the years and as the Shia became stronger.
As for why Lady Fatimah (as) had ordered for her grave to be concealed, it was because this was a form of protest and making her voice heard that she objects to what has taken place regarding the caliphate and successorship of the Prophet (pbuh). Therefore, as long as the Muslim nation doesnt believe in what she believes in regarding the Prophets successorship, which results in the deprivation of the Muslim nation of many true Islamic teachings, the reason for the concealment of her grave will remain.
Another point is that the concealment of her grave is a strong barrier that doesnt allow the falsification of the history of early Islam, preventing people from totally denying her stance against the situation that had come up regarding the caliphate. The issue of her grave is a sign for those in search of the truth, guiding them across the sea of evil and corruption to the shore of salvation, unveiling the truth and completing Allahs (swt) proof regarding it.
Of course, since the approximate coordinates of her grave have been mentioned, people can benefit from the areas close to her grave.
What was said, were only a few points that are supported by different clues and evidence, but that doesnt mean that these are all of the reasons, meaning that there are possibilities that there are other secrets behind this matter that might be unveiled in the future.
 See: Ibn Abil-Hadid, Sharh Nahjul-Balaghah, vol.16, pg.281; Sheykh Abdullah Naser, Mihnatu Fatimah bada Wafati Rasulillah, pp.197-206.
 According to hadiths, some of the places that her grave might possible be located are: between the Minbar and Mihrab of Masjidul-Nabi, Lady Fatimahs (as) home, and the graveyard of Baqi.