First, you are being misled by your wrong assumption that hippos have soft skin. Hippos have a 5 cm thick skin! For fun, here is a picture of a hippo skin.
They are big and pretty fast
An adult hippo weighs on average 1.5 and 1.3 tons for males and females respectively (with a record at 4.5 tons) and can run up to 30 km/h on land and up to 8 km/h in water (according to wikipedia > hippopotamus).
They have an aggressive nature
Hippos are aggressive animals (esp. males). Hippos kill about 500 people a year (against 1000 for crocodiles) according to this BBC article (but estimates seem to vary quite a bit from source to source).
They have serious teeth
Hippos have a big mouth with very long teeth. Lower canines are 50cm (19.7 inches) long (see wikipedia citing Estes 1991)!
Hippos live in herd
As suggested by @ChinmayKanchi in the comments, because hippos live in a herd, a crocodile that attacks a hippopotamus might have to deal with more than one enemy.
You can find here a video fight between a crocodile and a hippopotamus (thanks to @TahlaIrfan) and here is a video of a lion waking up a hippo. You will easily find other videos on YouTube.