Be careful not to confuse these as the same thing. You can disagree with someone and still go along with their idea. For example, lets say we were buying flowers for your mother together. You wanted to buy her red flowers, but I thought we should buy her purple flowers. I can still disagree with or dislike your idea of buying red flowers, but then go ahead and share the cost of the red flowers with you.

Usually, I don't use that expression in the negative sense. However, it is often used in the opposite way. People say, "He will go along with your ideas", but there is often a proviso or condition attached. For example, "I'll go along with that if you promise to pay half". "To go along" with something indicates agreement but not always wholehearted support. To me, in the negative sense, you would also need to state a reason. For example, "He doesn't go along with my ideas because he thinks they cost too much". Hope this helps