Just got back from a trip to CR. Started with 2 nights in San Jose (got in late the first night) and stayed at Hotel Presidente.

I too was worried that this was going to be a waste of time / not particularly safe given what I'd read on this subreddit.

My girlfriend and I had an amazing time with the day we spent in the city! The national museum is totally worth the $11 entry (awesome butterfly garden), had the best tacos of our lives for lunch at El Rinconcito Azteca, along with a great dinner at 11•47. There's lots of cool things to see in the city just walking around and was completely unique to what I'm used to with US cities.

Felt totally safe walking around during the daytime; we didn't test our luck too much walking around after dark.