I assume by $C(\mathbb{R})$ the question means the vector space of continuous real functions, but I'm not completely sure of that.
How might I go about formally proving this? Obviously I could say that there's no way you can get the graph of any of these functions through linear combinations of the other two, but that's not very formal. Writing out $$c_1x +c_2cosx+c_3\frac{x^2}{1+x^2} =0$$ isn't very helpful either as far as I can see. Any help is appreciated!
The equation you wrote must hold for any $x\in\mathbb{R}$. Put $x=0$ into the equation and you will get $c_2=0$. Then put $x=1$ and $x=-1$ to show that $c_1=c_3=0$.