Yes, that's correct. After expressions such as "I wouldn't be sure", "I don't think", or "I doubt", we often use the past tense to refer to a future situation from the speaker's point of view. So: "I wouldn't be sure that it was profitable in five years." is perfectly natural. You could also say: "I wouldn't be sure that it would be profitable in five years." if you want to emphasise the future outcome itself, but the second "would" is optional rather than required. In other words, the first version is completely grammatical and is probably the more natural choice in everyday English.

I agree with Gareth Todd.

Your phrase is okay but native speakers might say "I'm not sure that it will be profitable in 5 years." That's right, no 2nd would needed.