Normally it's thought that it's read as こきょう in general. When they read it ふるさと in 訓読み that Japanese reading, it especially means a faraway home which takes your important place in your mind. It is an emotional expression a bit. On the other hand, こきょう just means one's hometown/or birthplace. Though it's read each ふる and さと, they are not regular ways of reading and they're not on the kanji list of common use as well. So it's almost like an 当て字 reading that I feel. People can't tell is it read こきょう or ふるさと unless there's the furigana. So normally they just go with こきょう. I think that the Japanese way of reading makes it feels as so.

通常は「こきょう」と読みますが、「ふるさと」とも読まれます。ただ、「ふるさと」の最も一般的な漢字は「古里」です。 新聞等では 故郷（こきょう） 古里（ふるさと） としているところが多いようです。

どちらもよく使うので選ぶことは難しいですが、私がこの「故郷」という文字を見たときにパッと浮かんだのは「こきょう」です。

In my personal opinion, you more often write it in hiragana rather than in kanji if you mean "ふるさと".

Hometown is infinitely more used in media and common speech, I feel. Probably. Maybe.