First Age: Eärendil goes to Valinor and most of the Valar want him dead (correct me if I'm wrong) for daring to step foot on their soil.
Second Age: Manwë strikes Númenor with Thunder and Lightning instead of sending emissaries, killing many men invoking Ar-Pharazôn to attack Valinor.
Can anyone shed some light as to why the Valar acted this way toward them?
No. The Valar were looking out for Men as best they could, but they were hesitant to get very involved, because of the mortal nature of Men and their prior experience with Elves. Remember that Men very quickly fell from grace, as well, so they were in a 'state' more like the rebellious Noldor than they were, say, the Vanyar.
To Hildórien there came no Vala to guide Men, or to summon them to dwell in Valinor; and Men have feared the Valar, rather than loved them, and have not understood the purposes of the Powers, being at variance with them, and at strife with the world. Ulmo nonetheless took thought for them, aiding the counsel and will of Manwë; and his messages came often to them by stream and flood. But they have not skill in such matters, and still less had they in those days before they had mingled with the Elves.
(Silmarillion, "Of Men")
Eärendil was not specifically targeted for stepping foot on Valinor - mortal men and Noldor were banned from Valinor, the former for a pretty good reason (very bad things can result from Men spending too much time in Valinor), and the latter because of their murder and rebellion. Earendil was actually a double offender.
It is told among the Elves that after Eärendil had departed, seeking Elwing his wife, Mandos spoke concerning his fate; and he said: ‘Shall mortal Man step living upon the undying lands, and yet live?’ But Ulmo said: ‘For this he was born into the world. And say unto me: whether is he Eärendil Tuor's son of the line of Hador, or the son of Idril, Turgon's daughter, of the Elven-house of Finwë?’ And Mandos answered: ‘Equally the Noldor, who went wilfully into exile, may not return hither.’
But when all was spoken, Manwë gave judgement, and he said: ‘In this matter the power of doom is given to me. The peril that he ventured for love of the Two Kindreds shall not fall upon Earendil, nor shall it fall upon Elwing his wife, who entered into peril for love of him; but they shall not walk again ever among Elves or Men in the Outer Lands. And this is my decree concerning them: to Earendil and to Elwing, and to their sons, shall be given leave each to choose freely to which kindred their fates shall be joined, and under which kindred they shall be judged.’
As you can see, only the Doomsman Mandos said anything about it, and Manwë's "punishment" was very light, given that Elves no longer went from Valinor to Middle-earth except by special arrangement anyway.
In the case of Númenor, Manwë did send many emissaries. Eru and the Valar did not destroy Númenor until they actually landed on Valinor, giving them every chance to repent and turn back.
First Manwë sent messengers:
The Eldar reported these words to the Valar, and Manwë was grieved, seeing a cloud gather on the noontide of Númenor. And he sent messengers to the Dúnedain, who spoke earnestly to the King, and to all who would listen, concerning the fate and fashion of the world.
Then Manwë effectively sanctioned them, after they began persecuting the faithful and committing various other crimes or sins:
This was known to the kings, but they hindered it not, so long as the Elendili departed from their land and did not return; for they desired to end all friendship between their people and the Eldar of Eressëa, whom they named the Spies of the Valar, hoping to keep their deeds and their counsels hidden from the Lords of the West But all that they did was known to Manwë, and the Valar were wroth with the Kings of Númenor, and gave them counsel and protection no more; and the ships of Eressëa came never again out of the sunset, and the havens of Andúnië were forlorn.
Then he sent his lightning-warnings:
And out of the west there would come at times a great cloud in the evening, shaped as it were an eagle, with pinions spread to the north and the south; and slowly it would loom up, blotting out the sunset, and then uttermost night would fall upon Númenor. And some of the eagles bore lightning beneath their wings, and thunder echoed between sea and cloud.
Then men grew afraid. ‘Behold the Eagles of the Lords of the West!’ they cried. ‘The Eagles of Manwë are come upon Númenor!’ And they fell upon their faces.
(all from Silmarillion, "Akallabeth")
The Númenóreans had every chance to repent and chose not to.
The Valar only permitted elves setting foot on their continent of Aman. That is, apart from their own people, i.e. faithful Ainur (Valar and Maiar), of course. Those who participated in the Noldor rebellion had their permission to visit Aman revoked.
In any case, they were very harsh when it came to not letting those without permission to set foot on their continent, and Mandos would by his nature almost definitely be the harshest Vala of all (at least the harshest non-evil Vala). Eärendil would have been trespassing on blessed soil, hence the reaction from Mandos (fortunately, the Valar were moved by his plea). That does not mean they hated Men in general.
Still, my overall impression of the work is that the firstborn (elves) were favoured over the secondborn (Men), or any of the other free peoples for that matter. That is, favoured by the Valar, generally speaking.
The Valar viewed Men as unlike themselves, which was true. But at the same time they tried, at least in their own minds, to save them from darkness. Although, how well they did at this task is a matter of some debate, especially in the First Age.
While Eärendil could be said to be under the Ban of the Valar against the Noldor, as he was descended from them through his mother Idril Celebrindal, the rest of the actions of the Valar against Men in my mind showed an unwillingness to really try to get to know them or understand them.
While the Valar fought a war for the Elves against Melkor prior to their awakening, this war greatly damaged the Earth. It is for this reason they refused to do the same for Men. However, this reasoning is called into question both in how Ulmo gave his warning to Turgon about salvation being in the West and the actual aftermath of the War of Wrath being the complete destruction of Beleriand.
But the main reason I call into question the Valar's opinion of Men is in how they decided to place them under the same Doom they placed the Noldor. And therefore either Men had one of two choices. Beg with the Noldor for the Valar's pardon or fall under the domination of Morgoth.
