In the Talmud (Chulin 10a), Chazal taught that one should not drink water, wine or milk from containers that were left uncovered because a snake and its venom might have gotten into the drink and it will cause the person danger. Today, snakes are not commonly found and the Matei Yehonoson 116:1 says there is a heter to drink from uncovered vessels if no snakes are around, adding that one may be lenient because at the time of the halacha it was only made in a place where snakes were common. Nevertheless, I know people who continue to be stringent on this practice, even covering their water glass between sips. While I understand that poskim are stringent with regard to water left out overnight (see, e.g., Kitzur Shulchan Aruch 33:5), why should anyone need to be stringent during the course of a meal, when a snake would not likely crawl into a water goblet on a Shabbos table without notice?
Rivevos Ephraim 5:11 writes that in Sefer Halichos V'Hanahagos page 59 (Rav Eliyashiv) was Makpid to cover drinks. He brings a story were he covered his drink when he left the room for a second even with someone else there. He also brings a story which happened on Purim where he left room then came back and said don't drink the wine because it was left uncovered .see it inside.
Terumoth 8:4 implies that the drink would only have to be unobserved for a short time to be forbidden:
כַּמָּה יִשְׁהוּ וְיִהְיוּ אֲסוּרִין? כְּדֵי שֶׁיֵּצֵא הָרַחַשׁ מִמָּקוֹם קָרוֹב וְיִשְׁתֶּה:
How long must they be left [uncovered] for them to become forbidden? As long as [it would take] for a [creature] to come out from a nearby place and drink [from it].
The Bavli (Chullin 10a) seems to only extend this allowable period slightly:
וכמה "מקום קרוב"? א"ר יצחק בריה דרב יהודה: כדי שיצא מתחת אוזן כלי וישתה
And how far away is considered a "nearby place"? Rav Yitzḥak son of Rav Yehuda said: [Even a period equivalent to] the time [necessary so] that it could emerge from beneath the handle of [the] vessel and drink.
ישתה" - הא קא חזי ליה? אלא ישתה ויחזור לחורו":
[The Gemara asks: If it is only the time necessary for the creature to emerge and] drink, doesn’t one see [the creature drink, in which case there is no uncertainty]? Rather, [it is a period equivalent to the time necessary for a creature to emerge from a proximate place,] drink, and return to its hole. [If one left exposed liquid unattended for that interval, it is possible that the creature drank the liquid unseen by the owner of the liquid.]
Have you ever thought of snakes and their venom as people and their poisons? Perhaps the stringency should remain in place, as although snakes in their reptile form are not as common as they once were, the poison of people, is evermore prevalent and all the more so, regarding politics and people of power and the possible covert demise of your adversary. Kings often employed, tasters to taste their food and drink, in case a lethal poison had been introduced to their wine or water. As far as I know, snakes don't even have affinity with liquid substances within jars, but people do.
The Rambam brings this halacha in Hilchos Rotzeiach (chap 11:4), meaning that he believed that it was assur due to it being an actual sakana, and not for any ethical/mystical/spiritual reason. (Just as the gemarah in Chulin says - its a sakanah. The Shulchan Aruch does not bring down this halacha at all. I would note that the germ theory of disease was not discovered until 1900. At the time of Chazal and the Rishonim they knew that drinking water sometimes made people sick, but they did not know why. (See Dr.Chaim Soloveichic's Yayin Nesech Bemay Habanunim - thats why they drank so much wine - it did not make people sick).
In searching for a clue as to why it made people sick they assumed (based on the best scientific knowledge of their time) that it was due to a snake "o kyotze bo" that poisoned the liquid.
A Rationalist would use chazal's basic idea, ie. that its assur to do things that are dangerous (smoking, bungee jumping etc) but not necessarily be careful about the specific sakanah of uncovered liquid. A non-rationalist, would be doing a "minhag chassidus" by following this rule.