With the tip given by lulu you have $gcd(2^{2^{n+1}}-1,2^{F_n-1}-1)=2^{gcd(2^{n+1},F_n-1)}-1=2^{gcd(2^{n+1},2^{2^{n}})}-1$. Notice that for all $n \in \mathbb{N}$ $n+1\leq 2^n$(use induction to see this). Hence $2^{n+1} \mid 2^{2^n}$ and $gcd(2^{n+1},2^{2^{n}})=2^{n+1}$. So, $gcd(2^{2^{n+1}}-1,2^{F_n-1}-1)=2^{2^{n+1}}-1$ and we have that $2^{2^{n+1}}-1 \mid 2^{F_n-1}-1$.
Another try
Notice (again) that $n+1\leq 2^n$. Hence there is some $k \in \mathbb{N}$ such that $(n+1)+k=2^n$. Then $2^{2^n}=2^{(n+1)+k}=2^{n+1} \cdot 2^k$. Notice then that
$$
2^{F_n-1}-1=2^{2^{2^n}}-1=2^{2^{n+1} \cdot 2^k}-1=(2^{2^{n+1}})^{2^k}-1.
$$
So, to prove that $2^{2^{n+1}}-1 \mid 2^{F_n-1}-1$ is equivalent to prove that $2^{2^{n+1}}-1 \mid (2^{2^{n+1}})^{2^k}-1$. Now call $t=2^{2^{n+1}}$ and you need to prove that $t-1 \mid t^{2^k}-1$. Can you use long division to finish this?