[clause],+ 只是 + [reservation]
[subject] + 只是 + [verb phrase / noun]
At the head of a second clause, 只是 adds a reservation to what came first: "it's just that", "only". The first clause stays the main point; the 只是 clause is the one small problem.
但是 sets up a real contrast and makes the second clause the point. 只是 is softer and keeps the weight on the first clause.
不过 is close to 只是 in tone.
Inside a clause, 只是 before a verb phrase or a noun means "only", "merely" – nothing more than this.
只 + verb + object limits the object: only this, nothing else. 只是 limits the whole action: only doing this, nothing more serious.