"Why are the Scots so frightened at not being able to vote on matters that are only applicable to England?"
The position is more subtle than that. The complaint the SNP have is that the decision over what counts as "matters only applicable to England" will be taken out of their hands. In the last few parliaments, SNP members have opted to stay out of bills that, in their judgment, had no impact on Scotland. So although the anomaly still exists in theory, it hasn't cropped up in practice.
The problem comes when there are bills that have an indirect impact on Scotland, by changing laws that impact upon funding, for example. In the new rules, apparently it would be up to the Speaker as to whether or not Scottish MPs will get to vote (or, rather, to have a vote that counts at the key stages) on these matters.
On the other hand, the SNP can try to persuade the Speaker that these bills do have an impact on Scotland, and I would be surprised if he didn't accept their position. And anyway the solution the SNP had in place, where it was their discretion, is not ideal either. It's really better either to bring the UK back together properly or to break it up properly (as a federal system or as full-blown independence). Half-way house solutions like EVEL are messy and inadequate.