Fundamentalists (those who accept the fundamental principles of a faith) are always viewed as intolerant by liberals. You don't accept the fundamental truths of Hinduism as to do so would require you to reject sex for pleasure and reject same gender sexual activity. Hinduism may not take a stance against same gender sexual activity, however, Hinduism teaches the body is corrupt and the way to be one with your god is to reject earthly pleasure.
Many gay men and lesbian women find Hinduism appealing because it has evolved over time and as such there are very few absolute truths. Since Hinduism believes in reincarnation you believe you get many chances in multiple lives to attain perfection.
Your love story about Shiva and Vishnu is an example of how the original account has evolved. The original account states Vishnu changed gender; you teach Vishnu remained a mental male and thereby became a transsexual. No absolutes, therefore you can change ancient accounts to justify the way you live. You and many see this myth as a justification for homosexual love and for the reason some experience gender confussion.
Hinduism evolved from more ancient religions, which were incorporated into one faith. There are elements of Taoism, Pantheism, Animism, and .etc combined in an attempt to explain our existance and how to attain Nirvana. In reality what you believe is you can do as you please, seek pleasure where you can find it, and if you screw up you get another chance. What this does is remove personal responsibility for your actions. What this ignores is the Taoist concept of balance in the universe or the ying/yang of all that exists.
Gen 1:26-27
27 And God created man in His own image, in the image of God He created him; male and female He created them. NAS
Balance is found in God's creation, a balance man has perverted for personal pleasure.