A typical naive index won't help with my regular expression based queries, which aren't easily accelerated by an index. Or given an in-memory index, you've just increased memory use from O(1) to O(N), and I'll OOM on large files. Perhaps you'll throw a database at the problem, complicating I/O (especially when the data is generated/accessed by third party tools that aren't database based), tying me to yet another library's update cycle, and perhaps forcing me to tackle the additional problem of cache invalidation. Perhaps I need reverse lookups, in which case whatever forward indexing I might've pessemistically added ahead of time will be of no help at all.
If it'a a 5 second "this is probably the right choice" kneejerk reaction, maybe it's fine. Or if you're google indexing the internet, I suppose. But I am frequently plagued by shit, buggy, useless indexes that merely distract from the proper alexanderian solution to the gordian knot - brute force - wasting more time than they ever saved, for both people and CPUs.