what do you think is better? i heard that bassoon shouldnt be used in Baroque bass lines

Blasphemy! Not to mention absolutely baseless and untrue in general...

There is absolutely no reason why not. Many a score of baroque music I have seen which lists the bassoon as part of the continuo in movements without an obligato part.

Not to mention that the baroque is typically flexible when it comes to instrumentation.

I actually think the bassoon is better, but that's probably because I used to play it

I presume the original question refers to trio sonatas or other small scale works. A baroque bassoon would be OK in most contexts. A modern bassoon, with its more penetrating timbre, would be fine with oboes, possibly with flutes; I would prefer 'cello with violins.

In the baroque orchestra, 'cello, double bass and bassoon were all regular members of the bass section, and AFAIK it is legitimate to use a bassoon even if it is not specifically mentioned.

i dont think any one would care as long as you used baroque bassoons

I think Cello will fits better in Baroque string orchestras, because it is both strings. ^^I love cello.

Perhaps cello is more common and more suited especially to smaller groups. There are larger works like the Brandenburg Concerto 1 that has a bassoon on the continuo, and a lot of other wind instruments. It really depends on the instrumentation around the piece and what fits best.