"I understand where you're coming from" may or may not imply that you agree. It's perfectly common to say something like, "While I understand where you're coming from, it's still not going to work because..."
If you want make it more clear that you don't agree, you could say "I hear what you're saying [but...]" Similarly, the British set phrase "I hear what you say," is used to express explicit disagreement. (American speakers do not have a similarly explicit phrase, which can cause cross-cultural misunderstandings.)
The use of "hear" instead of "understand" expresses only, "I have received the idea you're trying to communicate." Consider this entry from Macmillan dictionary:
- I hear you
- I hear you or I hear what you're saying: used for telling someone that you understand their opinion, especially when you disagree with it
- used for agreeing with what someone says
This entry lists "I hear you" as potentially ambiguous (depending on context), but "I hear what you're saying" as mostly disagreeing.
It's a bit confusing, since these kinds of phrases are used to avoid discussing whether you agree or disagree. As an American speaker, I find the verb "understand" to be more sympathetic (and therefore more like to express agreement) than the more mechanical verb "hear."