Learn Dutch: Wij maken samen muziek. - We make music together.

Because the subject is Wij (we), which is plural. In Dutch, present tense plural verbs always take the full infinitive (dictionary) form, which almost always ends in -en.

Why is samen (together) in the middle of the sentence instead of at the end?

Dutch word order places adverbs like samen before the direct object (muziek). While in English you say 'We make music together', in Dutch the order is closer to 'We make together music'.

Why does maken have only one a if the vowel is pronounced long?

In Dutch, syllables ending in a single vowel are 'open' and automatically have a long sound. When you divide the word into syllables (ma-ken), the first syllable ends in a, so you only need one letter to get the long sound.

Could I use we instead of wij in this sentence?

Yes! We is the normal, unstressed word for 'we', while wij puts a little more emphasis on who is doing the action. Both are perfectly fine here and both take the plural verb maken.