According to the rules of Hepburn, (http://www.halcat.com/roomazi/doc/hep3.html) しいたけ is correctly romanized as "shiitake". What is the correct romanization of イー as in シート? Should it be "shiito" or "shīto" or "shi-to"?
More generally, the 長音 "ー" is always romanized with a macron over the vowel before it. (Reference: Kenkyūsha's New Japanese-English Dictionary)
(Other systems (I stick to Wāpuro rōmaji) use si for し, whence si-to. Kunrei-shiki uses a circumflex and would romanize シート to sîto.)