It's location seems perfect for a Mediterranean empire. It's close to Greece, Asia Minor, Egypt and the Levant.
Maybe even better situated than Constantinople.
Though in my minor education about the Romans I've never read a lot about it.
Was it used as a military or administrative centre?
If not, why not?
Crete was conquered by the Romans in 67 BC, and under Augustus the important town of Gortyn (famous for the ancient law tablets found there) was made capital of the province Creta et Cyrenae, which encompassed the island and the northafrican area of the Cyrenaica. So it was an administrative centre of at least local importance, a senatorial province, governed by a proconsul of praetorian rank. In the provincial reorganization of 295-7, Crete was made into a single equestrian province under the diocese of Moesia, elevated by Constantine again to a senatorial province in the diocese of Macedonia.
Crete had lost a lot of the importance it held in the Minoan Age (you can already tell how important Crete was, because this culture and time period was named after King Minos of Crete) during classical times, but came back into focus during the hellenic age as a hub and recruitment centre for mercenaries - but also as a centre for piracy. Cretan mercenaries fought in many wars of the hellenistic period. Cretan archers were among the most famous ranged troops of antiquity, and part of the 'caesarian' auxiliary trifecta of balearic slingers, numidian cavalry and cretan archers he had with him in Gaul. The Senate used them against C. Gracchus, too. As such Crete was also of limited importance during the civil wars, Pompey raised troops and received archers and grain from Crete. Marcus Antonius gifted some of it to Cleopatra.
Crete enjoyed an extraordinarily long period of peace and growth from Roman conquest up unti the 7th century (though the governor at Gortyn had to deal with the Garamantes in the mainland at Cyrenae), and Crete saw growing trade and prosperity. One thing Crete was famous for were healing herbs, some of which were endemic to Crete (like origanum dictamnus / hop majoram). Pliny mentions several times in his natural history that the best speciments of diverse plants and herbs come from Crete, for example Anise, or Origanum:
> But the best kind of all is that of Crete, for it has a particularly agreeable smell [n.h. XX, 69]
Galen also mentions the importance of Crete as origin of healing herbs, and how they were exported from there to all over the mediterranean (with the emperor, of course, getting his share via his procurators). Other important export goods of Crete were oil and especially wine (another thing Crete was famous for); so while at first the loss of lucrative mercenary contracts meant economic hardships for Crete, in general Roman times saw an economic revival of the island, with increasing wealth being evident in the archaeological record of the 2-3rd century. Export of herbs, spices and wine was dominant, and Crete was famous especially for those - and important as the only source of some of the best herbs and spices. Cretan auxiliary archers also remained an important aspect, until byzantine times.
Edit: spelling
In Knossos there were some Roman officials stationed but nothing to suggest that it was an administrative centre, as you put it, and certainly not a military base.
However, the main imperial hub in Crete was not Knossos but Gortyna. Here there were public buildings, Roman governors, administrative personnel, and Italian traders and merchants. This suggests that there was an Imperial presence on Crete but was mostly centred in Gortyna. Gortyna's port on the south was placed strategically on the trade route between Egypt and Rome, and therefore had economic importance, exporting wine quite heavily. There may have also been copper mines in Kandanos in Western Crete, therefore having some, although small, economic importance.