Hi there! I can offer you a partial response based on my knowledge of the ancient Near East, though I must emphasize that I am not an expert on this particular topic.

From the outset, we should distinguish between "homophobia" and "intolerance of same-sex acts," since homosexuality (as most conceive of it today) is a relatively recent construct. R. B. Parkinson explains the issue quite succinctly:

'Homosexuality' is a modern scientific construct, as is the division of sexuality into two (largely exclusive) categories of 'homosexuals' and 'heterosexuals', although historical evidence is sufficient to show that people who have same-sex relationships are not restricted to the modern world... It is now widely accepted that sexuality as a dominant characterising force was not recognised in the ancient world: sexual preferences were acknowledged, but only as one would recognise someone's taste in food without characterising him or her on that basis as a member of a sub-species of mankind. In Europe and the Mediterranean, personal identity seems not to have been defined in terms of sexual preferences before at least the seventeenth century AD, and 'homosexual' misdeeds were viewed as part of fleshly weakness to which all people were prone.

Parkinson goes on to show how the literature of Middle and New Kingdom Egypt evaluated same-sex acts between males in terms of "passive" and "active" roles. "Passive" participation meant "physical weakness" and the "abandoning a man's proper gender role for a 'womanly' one," whereas "active" participation may have expressed dominance or power. Consequently, these relationships always involved the "denigration of a weaker male."^1

The Middle Assyrian Laws (second half of the second millennium) seem to have approached same-sex acts from a similar context. To quote the laws themselves:

§18 If a man says to his comrade, either in private or in a public quarrel: "Everyone has sex with your wife, I can prove the charges," but he is unable to prove the charges and does not prove the charges, they shall strike him 40 blows with rods; he shall perform the king's service one full month; they shall cut off (his hair?) and he shall pay one talent of lead.

§19 If a man furtively spreads rumors about his comrade, saying: "Everyone has sex with him," or in a quarrel in public says to him, "Everyone has sex with you, I can prove the charges," but he is unable to prove the charges and does not prove the charges, they shall strike that man 50 blows with rods; he shall perform the king's service for one full month; they shall cut off (his hair?) and he shall pay one talent of lead.

§20 If a man has sex with his comrade and they prove the charges against him and find him guilty, they shall have sex with him and they shall turn him into a eunuch.^2

First, note that §19 meted out a slightly more severe punishment than §18 (ten additional blows). Second, as Martti Nissinen points out, §19 "refers to the shame of consenting to homosexual acts as the passive partner, at least if this happens repeatedly and voluntarily." Third, §20 implies that the sex itself was not necessarily immoral (someone would have to engage in sex with the "perpetrator" in order to carry out the punishment). Why did these rules exist? According to Nissinen:

The Middle Assyrian Laws assume that one partner actively lies on top of the other. This becomes criminal in the case when the object is a tappā’u, a man of equal social status, or a man who was otherwise socially involved with the perpetrator, like a neighbor or business partners... Penetrating a tappā’u was tantamount to rape and deliberate disgrace, because the penetrating partner effects a change in the other partner's role from active (male) to passive (female). Castration as a punishment was obviously intended not only to prevent the crime from happening again but also to alter permanently the role of the man who committed it. Many other texts take the raping of a man as an ultimate act of disgrace, which illuminates the role-division presumed in the Laws.^3

The Levitical prohibitions against homosexual acts between males (Leviticus 18:22 and 20:13) may reflect the same understanding of social relations. Thus, the immoral aspect involves the denigration of another man's status, not the sex itself. This point has been emphasized by Jerome Walsh:

The two legislative texts in Lev 18:22 and 20:13 have very narrow and very precise purview. They envisage one situation only: anal intercourse between two men, one of whom is a free adult Israelite and takes the passive sexual role of being penetrated by the other. The underlying system of social values within which such laws should be understood is the gender construction of maleness in a society where honor and shame are foundational social values. The male sexual role is to be the active penetrator; the passive role of being penetrated brings shame to a man (at least to a free adult male citizen) who engages in it and [...] also to the one who penetrates him.^4

Although these explanations remain open to challenge, they do provide appropriate contexts for interpreting same-sex relations in ancient Near Eastern texts. I welcome any alternative views! :)

 

Footnotes:

^1 R. B. Parkinson, "'Homosexual' Desire and Middle Kingdom Literature," Journal of Egyptian Archaeology 81 (1995): 57-76 (quotes from 58f. and 74).

^2 An alternate (though virtually identical) translation is available in Martha T. Roth, Law Collections from Mesopotamia and Asia Minor, 2nd ed., SBLWAW 6 (Atlanta: Society of Biblical Literature and Scholars Press, 1995). The quotations here come from Martti Nissinen (cited below).

^3 Martti Nissinen, Homoeroticism in the Biblical World: A Historical Perspective, trans. Kirsi Stjerna (Minneapolis: Fortress Press, 1998), 25f.

^4 Jerome T. Walsh, "Leviticus 18:22 and 20:13: Who Is Doing What to Whom?," Journal of Biblical Literature 120, no. 2 (2001): 201-9 (quote from 208). See also Nissinen, Homoeroticism in the Biblical World, 37-44.

This previous discussion includes examples relevant to your question. I think the short answer is "yes" but it was far from universal.

/r/AskAnthropology may be better suited to answer.

EDIT: May be /r/Anthropology, I can never remember.