I had the joy of being in a, brief, conversation with Spider Robinson a few years ago regarding exactly this question. Here's what I got out of it (TLDR at the bottom):
Turns out guideline for both SF and F are the same. Robinson made it clear, to me, regardless if you're talking about magic or technology, there has to be a set of defined rules. When you focus on the rules, the only difference between the two genres becomes the setting and available materials.
In Fantasy, magic without rules or structured behavior easily becomes laughable and cheesy. If you're in a story where all-of-a-sudden the main character whips out a massive damaging attack spell, you question "well why didn't you just use that before?" or "where the hell did that come from?" and "seriously, there's not consequence for using that?". It breaks the emersion. I know it's funny to talk about plausibility in a fantasy genre but it is there (or rather, it should be).
Good Fantasy sets up plausibility through structured rules about power balance and skills or object resources required to provide said magic. It should also include rules on how to "power up" the main character so bigger and better magic can be used. This then stops the generic "over kill" power from being over used and forces characters into conflicts about being able to use it. Fantasy has no established boundaries, you can setup any set of rules you want to establish the story.
Science Fiction sets up the same plausibility through the same use of rules but, basis for those rules often have pre established boundaries from real life. SF, even using advanced tech tends to have an unwritten expectation of being "realistic"; SF usually draw from existing resources, say mathematical and physical laws, and advances them into something we might be able to have or do in the future.
There are two types of SF I often see - the "hard core" SF is generated from existing laws and is often very ridged and structured around existing technology. And the lighter side of SF where the rules are established from existing tech but introduces new "magical" elements we haven?t dreamed of yet.
The again, there are plenty of SF stories that border on fantasy: when the tech goes beyond currently plausible technology and become magic? The reverse is true too. If a fantasy story doesn't use magic, then it's about the technology of the time -- but you would never call a medieval times based story science fiction, would you? So we're back to "setting" be the defining factor.
Regardless of genre, a good story is about the established rules. SF, I think, does a better job following these rules because it's more about physical object and physical resources. Whereas Fantasy and magic are often less tangible and have to be well established in advance for plausability.
--TLDR--
We're more critical of SF because we know that its story lines could exist some day. We're less critical of Fantasy because we know magic isn't real and never will be.
So really, the difference between the two is (IMO):
a) semantic - when does future tech become a type of magic for us? When did tech look like magic to people in the past?
b) setting and material - an enchanted and a light saber could be considered the same basic literary construct.
A good story should be able to be told in any genre with a few tweaks to the object details. Think about putting some of your favorite games into the opposite genre -- if the story was good would the setting make that much difference.
